Poetry update #553

github-actions · 2024-09-18T02:49:37Z

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commit 520a713 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:28:13 2024 +0200 fixes commit 227bf71 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:21:47 2024 +0200 record.change_entrytype(): run_quality_model() with set_prepared=True commit ba6ba8b Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:19:14 2024 +0200 record.remove_field_provenance_note(): also remove IGNORE:note commit 9f1c228 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:37 2024 +0200 no name-format defect for abbreviated names commit 8df75d4 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:02 2024 +0200 fix long line commit bbe831d Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:17:47 2024 +0200 update validation commit 12beaf5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:03:27 2024 +0200 update sync Signed-off-by: Gerit Wagner <[email protected]> commit 520192c Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:01:14 2024 +0200 update set_prepared in record.run_quality_model() commit ae108e5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:00:42 2024 +0200 crossref: raise ServiceNotAvailableException in crossref_query() commit 9d882f3 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 15:58:17 2024 +0200 prep polish: reset original state commit ddea08f Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:49 2024 +0200 [pre-commit.ci] pre-commit autoupdate (#556) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.7](astral-sh/ruff-pre-commit@v0.6.2...v0.6.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 77c055e Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:39 2024 +0200 update dependencies (#553) Co-authored-by: Poetry updater <[email protected]> commit d045a1d Author: Gerit Wagner <[email protected]> Date: Mon Sep 23 08:35:53 2024 +0200 fixes commit a112c20 Author: Carlo <[email protected]> Date: Fri Sep 20 07:38:10 2024 +0200 add command how to verify git credentials commit 81ebfb4 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 19:25:34 2024 +0200 move packages asciinema to comments commit 700c805 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 07:50:11 2024 +0200 testing/fixes commit 2605661 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 06:21:49 2024 +0200 tei_parser: set defaults commit cd42141 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:24:19 2024 +0200 upgrade: fix path-names in registry commit 36bfd05 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:08:04 2024 +0200 cli: add instructions commit ecbad8f Author: Gerit Wagner <[email protected]> Date: Sun Sep 15 10:51:48 2024 +0200 docs: add note on search udpates commit aa1b676 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 12:00:44 2024 +0200 docs: drop asciinema of package --init Signed-off-by:t Gerit Wagner <[email protected]> commit e791cc5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 09:41:21 2024 +0200 crossref: update printout commit ffd9628 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 14:02:14 2024 +0200 Reduce dependencies and switch to pydantic (#551) * move dependencies to arxiv and dedupe * pin numpy<2.0 * add bib-dedupe * switch to pydantic * switch to pydantic * update * sources. use relative filenames * update docs * fix mypy commit 1b84a37 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 10:13:18 2024 +0200 do not build paper in silent mode commit 910dffa Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:21 2024 +0200 add todo commit 7277c71 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:10 2024 +0200 fix import error: local_index.builder commit 026df75 Author: Gerit Wagner <[email protected]> Date: Wed Sep 11 07:09:15 2024 +0200 paper_md: stop container commit dc6ed46 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 11 06:19:15 2024 +0200 update dependencies (#550) Co-authored-by: Poetry updater <[email protected]> commit a4d12ec Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 20:40:56 2024 +0200 package_manager: packages do not necessarily start with "colrev." commit 5d23d21 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:36:08 2024 +0200 docker tests: remove intermediate containers commit 5142f4d Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:09:21 2024 +0200 docs: update path commit 2d6c2c2 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:08:34 2024 +0200 fix docker test commit 8c8f137 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 13:42:36 2024 +0200 docs: fix path commit 7b8c31e Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 09:23:19 2024 +0200 colrev project installation (making internal packages optional) (#530) * colrev project installation / make internal packages optional * drop optional extras from colrev * update * update gh-workflow Signed-off-by: Gerit Wagner <[email protected]> * format and docs * update upgrade * extract colrev-internal-package discovery * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * install packages after --add and init * add note on colrev install . to docs --------- Signed-off-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit bea78ac Author: Julian Prester <[email protected]> Date: Tue Sep 10 16:42:30 2024 +1000 Use posix paths for platform independence (#544) * Convert all paths for docker to posix * PRISMA: as_posix() * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * OCRMyPDF: as_posix() * fix prisma: path unlink() --------- Co-authored-by: Julian Prester <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> commit cd944e1 Author: Gerit Wagner <[email protected]> Date: Mon Sep 9 09:19:49 2024 +0200 europe_pmc: catch ValueError in lock.release() commit 685260b Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun Sep 8 14:44:24 2024 +0200 Update documentation (#548) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 046c09a Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:40 2024 +0200 Run Update documentation weekly to avoid many PRs commit 8fcb7e3 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:15 2024 +0200 refactor: pylint messages commit 3ea50f6 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:21:37 2024 +0200 crossref: catch Exception commit 163b5e1 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:19:55 2024 +0200 Update README.md commit 8f2460e Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:12:58 2024 +0200 update and rename workflows Signed-off-by: Gerit Wagner <[email protected]> commit c8bafc8 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:26:07 2024 +0200 data endpoint. add and commit commit b460db7 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:25:48 2024 +0200 init: check Docker available commit 85ea667 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 4 08:58:41 2024 +0200 update dependencies (#539) Co-authored-by: Poetry updater <[email protected]> commit 69d3eff Author: Gerit Wagner <[email protected]> Date: Wed Sep 4 07:41:42 2024 +0200 update relink_pdfs Signed-off-by: Gerit Wagner <[email protected]> commit fbd4d78 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 09:11:58 2024 +0200 add note on the order of pre/screening packages commit 09aa217 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 08:20:41 2024 +0200 update pdf text extraction commit 6588b68 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:26:21 2024 +0200 europe_pmc: refactor commit 9877da0 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:25:31 2024 +0200 crossref: refactor commit 7ba35df Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:35 2024 +0200 update print output commit dad30ad Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:05 2024 +0200 RecordNotInIndexException: ID mandatory commit 45deaa8 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:44 2024 +0200 pdf-get: fix symlinks after renamed dirs commit 91d5552 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:25 2024 +0200 load: warn on non-standardized fields (instead of raising exception) commit 829e036 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:20:57 2024 +0200 paper_md: fix path commit 5b4079e Author: Gerit Wagner <[email protected]> Date: Sat Aug 31 18:59:57 2024 +0200 sort SearchTypes commit 84d7901 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat Aug 31 16:20:02 2024 +0200 Update documentation (#528) Co-authored-by: github-actions <[email protected]>

commit d9a1a8a Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:33:22 2024 +0200 fix arxiv: pyproject.tomlÄ commit 38552d1 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:33:06 2024 +0200 fix naming conventions commit 6831e5b Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:07:16 2024 +0200 fix naming conventions commit a4aefd0 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:00:42 2024 +0200 install all-internal-packages for devcontainer (pylint) commit 5323329 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:57:18 2024 +0200 temporarily remove genai commit 520a713 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:28:13 2024 +0200 fixes commit 227bf71 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:21:47 2024 +0200 record.change_entrytype(): run_quality_model() with set_prepared=True commit ba6ba8b Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:19:14 2024 +0200 record.remove_field_provenance_note(): also remove IGNORE:note commit 9f1c228 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:37 2024 +0200 no name-format defect for abbreviated names commit 8df75d4 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:02 2024 +0200 fix long line commit bbe831d Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:17:47 2024 +0200 update validation commit 12beaf5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:03:27 2024 +0200 update sync Signed-off-by: Gerit Wagner <[email protected]> commit 520192c Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:01:14 2024 +0200 update set_prepared in record.run_quality_model() commit ae108e5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:00:42 2024 +0200 crossref: raise ServiceNotAvailableException in crossref_query() commit 9d882f3 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 15:58:17 2024 +0200 prep polish: reset original state commit ddea08f Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:49 2024 +0200 [pre-commit.ci] pre-commit autoupdate (#556) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.7](astral-sh/ruff-pre-commit@v0.6.2...v0.6.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 77c055e Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:39 2024 +0200 update dependencies (#553) Co-authored-by: Poetry updater <[email protected]> commit d045a1d Author: Gerit Wagner <[email protected]> Date: Mon Sep 23 08:35:53 2024 +0200 fixes commit a112c20 Author: Carlo <[email protected]> Date: Fri Sep 20 07:38:10 2024 +0200 add command how to verify git credentials commit 81ebfb4 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 19:25:34 2024 +0200 move packages asciinema to comments commit 700c805 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 07:50:11 2024 +0200 testing/fixes commit 2605661 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 06:21:49 2024 +0200 tei_parser: set defaults commit cd42141 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:24:19 2024 +0200 upgrade: fix path-names in registry commit 36bfd05 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:08:04 2024 +0200 cli: add instructions commit ecbad8f Author: Gerit Wagner <[email protected]> Date: Sun Sep 15 10:51:48 2024 +0200 docs: add note on search udpates commit aa1b676 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 12:00:44 2024 +0200 docs: drop asciinema of package --init Signed-off-by:t Gerit Wagner <[email protected]> commit e791cc5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 09:41:21 2024 +0200 crossref: update printout commit ffd9628 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 14:02:14 2024 +0200 Reduce dependencies and switch to pydantic (#551) * move dependencies to arxiv and dedupe * pin numpy<2.0 * add bib-dedupe * switch to pydantic * switch to pydantic * update * sources. use relative filenames * update docs * fix mypy commit 1b84a37 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 10:13:18 2024 +0200 do not build paper in silent mode commit 910dffa Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:21 2024 +0200 add todo commit 7277c71 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:10 2024 +0200 fix import error: local_index.builder commit 026df75 Author: Gerit Wagner <[email protected]> Date: Wed Sep 11 07:09:15 2024 +0200 paper_md: stop container commit dc6ed46 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 11 06:19:15 2024 +0200 update dependencies (#550) Co-authored-by: Poetry updater <[email protected]> commit a4d12ec Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 20:40:56 2024 +0200 package_manager: packages do not necessarily start with "colrev." commit 5d23d21 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:36:08 2024 +0200 docker tests: remove intermediate containers commit 5142f4d Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:09:21 2024 +0200 docs: update path commit 2d6c2c2 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:08:34 2024 +0200 fix docker test commit 8c8f137 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 13:42:36 2024 +0200 docs: fix path commit 7b8c31e Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 09:23:19 2024 +0200 colrev project installation (making internal packages optional) (#530) * colrev project installation / make internal packages optional * drop optional extras from colrev * update * update gh-workflow Signed-off-by: Gerit Wagner <[email protected]> * format and docs * update upgrade * extract colrev-internal-package discovery * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * install packages after --add and init * add note on colrev install . to docs --------- Signed-off-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit bea78ac Author: Julian Prester <[email protected]> Date: Tue Sep 10 16:42:30 2024 +1000 Use posix paths for platform independence (#544) * Convert all paths for docker to posix * PRISMA: as_posix() * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * OCRMyPDF: as_posix() * fix prisma: path unlink() --------- Co-authored-by: Julian Prester <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> commit cd944e1 Author: Gerit Wagner <[email protected]> Date: Mon Sep 9 09:19:49 2024 +0200 europe_pmc: catch ValueError in lock.release() commit 685260b Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun Sep 8 14:44:24 2024 +0200 Update documentation (#548) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 046c09a Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:40 2024 +0200 Run Update documentation weekly to avoid many PRs commit 8fcb7e3 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:15 2024 +0200 refactor: pylint messages commit 3ea50f6 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:21:37 2024 +0200 crossref: catch Exception commit 163b5e1 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:19:55 2024 +0200 Update README.md commit 8f2460e Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:12:58 2024 +0200 update and rename workflows Signed-off-by: Gerit Wagner <[email protected]> commit c8bafc8 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:26:07 2024 +0200 data endpoint. add and commit commit b460db7 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:25:48 2024 +0200 init: check Docker available commit 85ea667 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 4 08:58:41 2024 +0200 update dependencies (#539) Co-authored-by: Poetry updater <[email protected]> commit 69d3eff Author: Gerit Wagner <[email protected]> Date: Wed Sep 4 07:41:42 2024 +0200 update relink_pdfs Signed-off-by: Gerit Wagner <[email protected]> commit fbd4d78 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 09:11:58 2024 +0200 add note on the order of pre/screening packages commit 09aa217 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 08:20:41 2024 +0200 update pdf text extraction commit 6588b68 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:26:21 2024 +0200 europe_pmc: refactor commit 9877da0 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:25:31 2024 +0200 crossref: refactor commit 7ba35df Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:35 2024 +0200 update print output commit dad30ad Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:05 2024 +0200 RecordNotInIndexException: ID mandatory commit 45deaa8 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:44 2024 +0200 pdf-get: fix symlinks after renamed dirs commit 91d5552 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:25 2024 +0200 load: warn on non-standardized fields (instead of raising exception) commit 829e036 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:20:57 2024 +0200 paper_md: fix path commit 5b4079e Author: Gerit Wagner <[email protected]> Date: Sat Aug 31 18:59:57 2024 +0200 sort SearchTypes commit 84d7901 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat Aug 31 16:20:02 2024 +0200 Update documentation (#528) Co-authored-by: github-actions <[email protected]>

commit 096ae8f Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 21:23:48 2024 +0200 merge main commit d9a1a8a Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:33:22 2024 +0200 fix arxiv: pyproject.tomlÄ commit 38552d1 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:33:06 2024 +0200 fix naming conventions commit 6831e5b Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:07:16 2024 +0200 fix naming conventions commit a4aefd0 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:00:42 2024 +0200 install all-internal-packages for devcontainer (pylint) commit 5323329 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:57:18 2024 +0200 temporarily remove genai commit 520a713 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:28:13 2024 +0200 fixes commit 227bf71 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:21:47 2024 +0200 record.change_entrytype(): run_quality_model() with set_prepared=True commit ba6ba8b Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:19:14 2024 +0200 record.remove_field_provenance_note(): also remove IGNORE:note commit 9f1c228 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:37 2024 +0200 no name-format defect for abbreviated names commit 8df75d4 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:02 2024 +0200 fix long line commit bbe831d Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:17:47 2024 +0200 update validation commit 12beaf5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:03:27 2024 +0200 update sync Signed-off-by: Gerit Wagner <[email protected]> commit 520192c Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:01:14 2024 +0200 update set_prepared in record.run_quality_model() commit ae108e5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:00:42 2024 +0200 crossref: raise ServiceNotAvailableException in crossref_query() commit 9d882f3 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 15:58:17 2024 +0200 prep polish: reset original state commit ddea08f Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:49 2024 +0200 [pre-commit.ci] pre-commit autoupdate (#556) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.7](astral-sh/ruff-pre-commit@v0.6.2...v0.6.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 77c055e Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:39 2024 +0200 update dependencies (#553) Co-authored-by: Poetry updater <[email protected]> commit d045a1d Author: Gerit Wagner <[email protected]> Date: Mon Sep 23 08:35:53 2024 +0200 fixes commit a112c20 Author: Carlo <[email protected]> Date: Fri Sep 20 07:38:10 2024 +0200 add command how to verify git credentials commit 81ebfb4 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 19:25:34 2024 +0200 move packages asciinema to comments commit 700c805 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 07:50:11 2024 +0200 testing/fixes commit 2605661 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 06:21:49 2024 +0200 tei_parser: set defaults commit cd42141 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:24:19 2024 +0200 upgrade: fix path-names in registry commit 36bfd05 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:08:04 2024 +0200 cli: add instructions commit ecbad8f Author: Gerit Wagner <[email protected]> Date: Sun Sep 15 10:51:48 2024 +0200 docs: add note on search udpates commit aa1b676 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 12:00:44 2024 +0200 docs: drop asciinema of package --init Signed-off-by:t Gerit Wagner <[email protected]> commit e791cc5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 09:41:21 2024 +0200 crossref: update printout commit ffd9628 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 14:02:14 2024 +0200 Reduce dependencies and switch to pydantic (#551) * move dependencies to arxiv and dedupe * pin numpy<2.0 * add bib-dedupe * switch to pydantic * switch to pydantic * update * sources. use relative filenames * update docs * fix mypy commit 1b84a37 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 10:13:18 2024 +0200 do not build paper in silent mode commit 910dffa Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:21 2024 +0200 add todo commit 7277c71 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:10 2024 +0200 fix import error: local_index.builder commit 026df75 Author: Gerit Wagner <[email protected]> Date: Wed Sep 11 07:09:15 2024 +0200 paper_md: stop container commit dc6ed46 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 11 06:19:15 2024 +0200 update dependencies (#550) Co-authored-by: Poetry updater <[email protected]> commit a4d12ec Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 20:40:56 2024 +0200 package_manager: packages do not necessarily start with "colrev." commit 5d23d21 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:36:08 2024 +0200 docker tests: remove intermediate containers commit 5142f4d Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:09:21 2024 +0200 docs: update path commit 2d6c2c2 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:08:34 2024 +0200 fix docker test commit 8c8f137 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 13:42:36 2024 +0200 docs: fix path commit 7b8c31e Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 09:23:19 2024 +0200 colrev project installation (making internal packages optional) (#530) * colrev project installation / make internal packages optional * drop optional extras from colrev * update * update gh-workflow Signed-off-by: Gerit Wagner <[email protected]> * format and docs * update upgrade * extract colrev-internal-package discovery * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * install packages after --add and init * add note on colrev install . to docs --------- Signed-off-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit bea78ac Author: Julian Prester <[email protected]> Date: Tue Sep 10 16:42:30 2024 +1000 Use posix paths for platform independence (#544) * Convert all paths for docker to posix * PRISMA: as_posix() * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * OCRMyPDF: as_posix() * fix prisma: path unlink() --------- Co-authored-by: Julian Prester <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> commit cd944e1 Author: Gerit Wagner <[email protected]> Date: Mon Sep 9 09:19:49 2024 +0200 europe_pmc: catch ValueError in lock.release() commit 685260b Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun Sep 8 14:44:24 2024 +0200 Update documentation (#548) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 046c09a Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:40 2024 +0200 Run Update documentation weekly to avoid many PRs commit 8fcb7e3 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:15 2024 +0200 refactor: pylint messages commit 3ea50f6 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:21:37 2024 +0200 crossref: catch Exception commit 163b5e1 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:19:55 2024 +0200 Update README.md commit 8f2460e Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:12:58 2024 +0200 update and rename workflows Signed-off-by: Gerit Wagner <[email protected]> commit c8bafc8 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:26:07 2024 +0200 data endpoint. add and commit commit b460db7 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:25:48 2024 +0200 init: check Docker available commit 85ea667 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 4 08:58:41 2024 +0200 update dependencies (#539) Co-authored-by: Poetry updater <[email protected]> commit 69d3eff Author: Gerit Wagner <[email protected]> Date: Wed Sep 4 07:41:42 2024 +0200 update relink_pdfs Signed-off-by: Gerit Wagner <[email protected]> commit fbd4d78 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 09:11:58 2024 +0200 add note on the order of pre/screening packages commit 09aa217 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 08:20:41 2024 +0200 update pdf text extraction commit 6588b68 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:26:21 2024 +0200 europe_pmc: refactor commit 9877da0 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:25:31 2024 +0200 crossref: refactor commit 7ba35df Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:35 2024 +0200 update print output commit dad30ad Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:05 2024 +0200 RecordNotInIndexException: ID mandatory commit 45deaa8 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:44 2024 +0200 pdf-get: fix symlinks after renamed dirs commit 91d5552 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:25 2024 +0200 load: warn on non-standardized fields (instead of raising exception) commit 829e036 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:20:57 2024 +0200 paper_md: fix path commit 5b4079e Author: Gerit Wagner <[email protected]> Date: Sat Aug 31 18:59:57 2024 +0200 sort SearchTypes commit 84d7901 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat Aug 31 16:20:02 2024 +0200 Update documentation (#528) Co-authored-by: github-actions <[email protected]> commit 9a0b265 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:53:19 2024 +0200 files_dir: stricter quality control commit ed28672 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:40:27 2024 +0200 add instruction to cli-validation commit 866ca2c Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:32:18 2024 +0200 sync with main commit 520a713 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:28:13 2024 +0200 fixes commit 227bf71 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:21:47 2024 +0200 record.change_entrytype(): run_quality_model() with set_prepared=True commit ba6ba8b Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:19:14 2024 +0200 record.remove_field_provenance_note(): also remove IGNORE:note commit 9f1c228 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:37 2024 +0200 no name-format defect for abbreviated names commit 8df75d4 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:02 2024 +0200 fix long line commit bbe831d Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:17:47 2024 +0200 update validation commit 12beaf5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:03:27 2024 +0200 update sync Signed-off-by: Gerit Wagner <[email protected]> commit 520192c Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:01:14 2024 +0200 update set_prepared in record.run_quality_model() commit ae108e5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:00:42 2024 +0200 crossref: raise ServiceNotAvailableException in crossref_query() commit 9d882f3 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 15:58:17 2024 +0200 prep polish: reset original state commit ddea08f Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:49 2024 +0200 [pre-commit.ci] pre-commit autoupdate (#556) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.7](astral-sh/ruff-pre-commit@v0.6.2...v0.6.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 77c055e Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:39 2024 +0200 update dependencies (#553) Co-authored-by: Poetry updater <[email protected]> commit d045a1d Author: Gerit Wagner <[email protected]> Date: Mon Sep 23 08:35:53 2024 +0200 fixes commit a112c20 Author: Carlo <[email protected]> Date: Fri Sep 20 07:38:10 2024 +0200 add command how to verify git credentials commit 81ebfb4 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 19:25:34 2024 +0200 move packages asciinema to comments commit 700c805 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 07:50:11 2024 +0200 testing/fixes commit 2605661 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 06:21:49 2024 +0200 tei_parser: set defaults commit cd42141 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:24:19 2024 +0200 upgrade: fix path-names in registry commit 36bfd05 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:08:04 2024 +0200 cli: add instructions commit ecbad8f Author: Gerit Wagner <[email protected]> Date: Sun Sep 15 10:51:48 2024 +0200 docs: add note on search udpates commit aa1b676 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 12:00:44 2024 +0200 docs: drop asciinema of package --init Signed-off-by:t Gerit Wagner <[email protected]> commit e791cc5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 09:41:21 2024 +0200 crossref: update printout commit ffd9628 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 14:02:14 2024 +0200 Reduce dependencies and switch to pydantic (#551) * move dependencies to arxiv and dedupe * pin numpy<2.0 * add bib-dedupe * switch to pydantic * switch to pydantic * update * sources. use relative filenames * update docs * fix mypy commit 1b84a37 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 10:13:18 2024 +0200 do not build paper in silent mode commit 910dffa Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:21 2024 +0200 add todo commit 7277c71 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:10 2024 +0200 fix import error: local_index.builder commit 026df75 Author: Gerit Wagner <[email protected]> Date: Wed Sep 11 07:09:15 2024 +0200 paper_md: stop container commit dc6ed46 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 11 06:19:15 2024 +0200 update dependencies (#550) Co-authored-by: Poetry updater <[email protected]> commit a4d12ec Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 20:40:56 2024 +0200 package_manager: packages do not necessarily start with "colrev." commit 5d23d21 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:36:08 2024 +0200 docker tests: remove intermediate containers commit 5142f4d Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:09:21 2024 +0200 docs: update path commit 2d6c2c2 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:08:34 2024 +0200 fix docker test commit 8c8f137 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 13:42:36 2024 +0200 docs: fix path commit 7b8c31e Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 09:23:19 2024 +0200 colrev project installation (making internal packages optional) (#530) * colrev project installation / make internal packages optional * drop optional extras from colrev * update * update gh-workflow Signed-off-by: Gerit Wagner <[email protected]> * format and docs * update upgrade * extract colrev-internal-package discovery * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * install packages after --add and init * add note on colrev install . to docs --------- Signed-off-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit bea78ac Author: Julian Prester <[email protected]> Date: Tue Sep 10 16:42:30 2024 +1000 Use posix paths for platform independence (#544) * Convert all paths for docker to posix * PRISMA: as_posix() * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * OCRMyPDF: as_posix() * fix prisma: path unlink() --------- Co-authored-by: Julian Prester <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> commit cd944e1 Author: Gerit Wagner <[email protected]> Date: Mon Sep 9 09:19:49 2024 +0200 europe_pmc: catch ValueError in lock.release() commit 685260b Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun Sep 8 14:44:24 2024 +0200 Update documentation (#548) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 046c09a Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:40 2024 +0200 Run Update documentation weekly to avoid many PRs commit 8fcb7e3 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:15 2024 +0200 refactor: pylint messages commit 3ea50f6 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:21:37 2024 +0200 crossref: catch Exception commit 163b5e1 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:19:55 2024 +0200 Update README.md commit 8f2460e Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:12:58 2024 +0200 update and rename workflows Signed-off-by: Gerit Wagner <[email protected]> commit c8bafc8 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:26:07 2024 +0200 data endpoint. add and commit commit b460db7 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:25:48 2024 +0200 init: check Docker available commit 85ea667 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 4 08:58:41 2024 +0200 update dependencies (#539) Co-authored-by: Poetry updater <[email protected]> commit 69d3eff Author: Gerit Wagner <[email protected]> Date: Wed Sep 4 07:41:42 2024 +0200 update relink_pdfs Signed-off-by: Gerit Wagner <[email protected]> commit fbd4d78 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 09:11:58 2024 +0200 add note on the order of pre/screening packages commit 09aa217 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 08:20:41 2024 +0200 update pdf text extraction commit 6588b68 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:26:21 2024 +0200 europe_pmc: refactor commit 9877da0 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:25:31 2024 +0200 crossref: refactor commit 7ba35df Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:35 2024 +0200 update print output commit dad30ad Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:05 2024 +0200 RecordNotInIndexException: ID mandatory commit 45deaa8 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:44 2024 +0200 pdf-get: fix symlinks after renamed dirs commit 91d5552 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:25 2024 +0200 load: warn on non-standardized fields (instead of raising exception) commit 829e036 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:20:57 2024 +0200 paper_md: fix path commit 5b4079e Author: Gerit Wagner <[email protected]> Date: Sat Aug 31 18:59:57 2024 +0200 sort SearchTypes commit 84d7901 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat Aug 31 16:20:02 2024 +0200 Update documentation (#528) Co-authored-by: github-actions <[email protected]> commit 2b765e4 Merge: 4944933 5c4117c Author: Gerit Wagner <[email protected]> Date: Sat Aug 31 18:32:36 2024 +0200 Merge branch 'main' into relax_prep commit 4944933 Author: Gerit Wagner <[email protected]> Date: Sat Aug 31 18:29:47 2024 +0200 update poetry.lock commit 20e00b5 Author: Gerit Wagner <[email protected]> Date: Wed Aug 28 18:40:16 2024 +0200 update validation commit cae8c98 Author: Gerit Wagner <[email protected]> Date: Wed Aug 28 18:12:59 2024 +0200 reorder imports commit 0cc6350 Author: Gerit Wagner <[email protected]> Date: Wed Aug 28 18:12:41 2024 +0200 remove record notes commit 9038f35 Author: Gerit Wagner <[email protected]> Date: Wed Aug 28 18:09:13 2024 +0200 add ref_check as a default package commit 4a13a14 Merge: 90ad50e b4be8af Author: Gerit Wagner <[email protected]> Date: Wed Aug 28 17:22:12 2024 +0200 Merge branch 'main' into relax_prep commit 90ad50e Author: Gerit Wagner <[email protected]> Date: Wed Aug 28 17:05:45 2024 +0200 record_test: ignore mypy errors commit 73a0653 Merge: 3ceb0d5 861b5a5 Author: Gerit Wagner <[email protected]> Date: Wed Aug 28 16:38:30 2024 +0200 Merge branch 'main' into relax_prep commit 3ceb0d5 Author: Gerit Wagner <[email protected]> Date: Fri Aug 23 18:38:52 2024 +0200 create package ref_check commit becd843 Author: Gerit Wagner <[email protected]> Date: Fri Aug 23 16:56:35 2024 +0200 has_fatal_quality_defects()

* has_fatal_quality_defects() * create package ref_check * record_test: ignore mypy errors * add ref_check as a default package * remove record notes * reorder imports * update validation * update poetry.lock * sync with main commit 520a713 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:28:13 2024 +0200 fixes commit 227bf71 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:21:47 2024 +0200 record.change_entrytype(): run_quality_model() with set_prepared=True commit ba6ba8b Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:19:14 2024 +0200 record.remove_field_provenance_note(): also remove IGNORE:note commit 9f1c228 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:37 2024 +0200 no name-format defect for abbreviated names commit 8df75d4 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:02 2024 +0200 fix long line commit bbe831d Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:17:47 2024 +0200 update validation commit 12beaf5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:03:27 2024 +0200 update sync Signed-off-by: Gerit Wagner <[email protected]> commit 520192c Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:01:14 2024 +0200 update set_prepared in record.run_quality_model() commit ae108e5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:00:42 2024 +0200 crossref: raise ServiceNotAvailableException in crossref_query() commit 9d882f3 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 15:58:17 2024 +0200 prep polish: reset original state commit ddea08f Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:49 2024 +0200 [pre-commit.ci] pre-commit autoupdate (#556) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.7](astral-sh/ruff-pre-commit@v0.6.2...v0.6.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 77c055e Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:39 2024 +0200 update dependencies (#553) Co-authored-by: Poetry updater <[email protected]> commit d045a1d Author: Gerit Wagner <[email protected]> Date: Mon Sep 23 08:35:53 2024 +0200 fixes commit a112c20 Author: Carlo <[email protected]> Date: Fri Sep 20 07:38:10 2024 +0200 add command how to verify git credentials commit 81ebfb4 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 19:25:34 2024 +0200 move packages asciinema to comments commit 700c805 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 07:50:11 2024 +0200 testing/fixes commit 2605661 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 06:21:49 2024 +0200 tei_parser: set defaults commit cd42141 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:24:19 2024 +0200 upgrade: fix path-names in registry commit 36bfd05 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:08:04 2024 +0200 cli: add instructions commit ecbad8f Author: Gerit Wagner <[email protected]> Date: Sun Sep 15 10:51:48 2024 +0200 docs: add note on search udpates commit aa1b676 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 12:00:44 2024 +0200 docs: drop asciinema of package --init Signed-off-by:t Gerit Wagner <[email protected]> commit e791cc5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 09:41:21 2024 +0200 crossref: update printout commit ffd9628 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 14:02:14 2024 +0200 Reduce dependencies and switch to pydantic (#551) * move dependencies to arxiv and dedupe * pin numpy<2.0 * add bib-dedupe * switch to pydantic * switch to pydantic * update * sources. use relative filenames * update docs * fix mypy commit 1b84a37 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 10:13:18 2024 +0200 do not build paper in silent mode commit 910dffa Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:21 2024 +0200 add todo commit 7277c71 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:10 2024 +0200 fix import error: local_index.builder commit 026df75 Author: Gerit Wagner <[email protected]> Date: Wed Sep 11 07:09:15 2024 +0200 paper_md: stop container commit dc6ed46 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 11 06:19:15 2024 +0200 update dependencies (#550) Co-authored-by: Poetry updater <[email protected]> commit a4d12ec Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 20:40:56 2024 +0200 package_manager: packages do not necessarily start with "colrev." commit 5d23d21 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:36:08 2024 +0200 docker tests: remove intermediate containers commit 5142f4d Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:09:21 2024 +0200 docs: update path commit 2d6c2c2 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:08:34 2024 +0200 fix docker test commit 8c8f137 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 13:42:36 2024 +0200 docs: fix path commit 7b8c31e Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 09:23:19 2024 +0200 colrev project installation (making internal packages optional) (#530) * colrev project installation / make internal packages optional * drop optional extras from colrev * update * update gh-workflow Signed-off-by: Gerit Wagner <[email protected]> * format and docs * update upgrade * extract colrev-internal-package discovery * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * install packages after --add and init * add note on colrev install . to docs --------- Signed-off-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit bea78ac Author: Julian Prester <[email protected]> Date: Tue Sep 10 16:42:30 2024 +1000 Use posix paths for platform independence (#544) * Convert all paths for docker to posix * PRISMA: as_posix() * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * OCRMyPDF: as_posix() * fix prisma: path unlink() --------- Co-authored-by: Julian Prester <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> commit cd944e1 Author: Gerit Wagner <[email protected]> Date: Mon Sep 9 09:19:49 2024 +0200 europe_pmc: catch ValueError in lock.release() commit 685260b Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun Sep 8 14:44:24 2024 +0200 Update documentation (#548) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 046c09a Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:40 2024 +0200 Run Update documentation weekly to avoid many PRs commit 8fcb7e3 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:15 2024 +0200 refactor: pylint messages commit 3ea50f6 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:21:37 2024 +0200 crossref: catch Exception commit 163b5e1 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:19:55 2024 +0200 Update README.md commit 8f2460e Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:12:58 2024 +0200 update and rename workflows Signed-off-by: Gerit Wagner <[email protected]> commit c8bafc8 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:26:07 2024 +0200 data endpoint. add and commit commit b460db7 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:25:48 2024 +0200 init: check Docker available commit 85ea667 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 4 08:58:41 2024 +0200 update dependencies (#539) Co-authored-by: Poetry updater <[email protected]> commit 69d3eff Author: Gerit Wagner <[email protected]> Date: Wed Sep 4 07:41:42 2024 +0200 update relink_pdfs Signed-off-by: Gerit Wagner <[email protected]> commit fbd4d78 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 09:11:58 2024 +0200 add note on the order of pre/screening packages commit 09aa217 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 08:20:41 2024 +0200 update pdf text extraction commit 6588b68 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:26:21 2024 +0200 europe_pmc: refactor commit 9877da0 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:25:31 2024 +0200 crossref: refactor commit 7ba35df Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:35 2024 +0200 update print output commit dad30ad Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:05 2024 +0200 RecordNotInIndexException: ID mandatory commit 45deaa8 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:44 2024 +0200 pdf-get: fix symlinks after renamed dirs commit 91d5552 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:25 2024 +0200 load: warn on non-standardized fields (instead of raising exception) commit 829e036 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:20:57 2024 +0200 paper_md: fix path commit 5b4079e Author: Gerit Wagner <[email protected]> Date: Sat Aug 31 18:59:57 2024 +0200 sort SearchTypes commit 84d7901 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat Aug 31 16:20:02 2024 +0200 Update documentation (#528) Co-authored-by: github-actions <[email protected]> * add instruction to cli-validation * files_dir: stricter quality control * merge main commit d9a1a8a Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:33:22 2024 +0200 fix arxiv: pyproject.tomlÄ commit 38552d1 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:33:06 2024 +0200 fix naming conventions commit 6831e5b Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:07:16 2024 +0200 fix naming conventions commit a4aefd0 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:00:42 2024 +0200 install all-internal-packages for devcontainer (pylint) commit 5323329 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:57:18 2024 +0200 temporarily remove genai commit 520a713 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:28:13 2024 +0200 fixes commit 227bf71 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:21:47 2024 +0200 record.change_entrytype(): run_quality_model() with set_prepared=True commit ba6ba8b Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:19:14 2024 +0200 record.remove_field_provenance_note(): also remove IGNORE:note commit 9f1c228 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:37 2024 +0200 no name-format defect for abbreviated names commit 8df75d4 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:02 2024 +0200 fix long line commit bbe831d Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:17:47 2024 +0200 update validation commit 12beaf5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:03:27 2024 +0200 update sync Signed-off-by: Gerit Wagner <[email protected]> commit 520192c Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:01:14 2024 +0200 update set_prepared in record.run_quality_model() commit ae108e5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:00:42 2024 +0200 crossref: raise ServiceNotAvailableException in crossref_query() commit 9d882f3 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 15:58:17 2024 +0200 prep polish: reset original state commit ddea08f Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:49 2024 +0200 [pre-commit.ci] pre-commit autoupdate (#556) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.7](astral-sh/ruff-pre-commit@v0.6.2...v0.6.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 77c055e Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:39 2024 +0200 update dependencies (#553) Co-authored-by: Poetry updater <[email protected]> commit d045a1d Author: Gerit Wagner <[email protected]> Date: Mon Sep 23 08:35:53 2024 +0200 fixes commit a112c20 Author: Carlo <[email protected]> Date: Fri Sep 20 07:38:10 2024 +0200 add command how to verify git credentials commit 81ebfb4 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 19:25:34 2024 +0200 move packages asciinema to comments commit 700c805 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 07:50:11 2024 +0200 testing/fixes commit 2605661 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 06:21:49 2024 +0200 tei_parser: set defaults commit cd42141 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:24:19 2024 +0200 upgrade: fix path-names in registry commit 36bfd05 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:08:04 2024 +0200 cli: add instructions commit ecbad8f Author: Gerit Wagner <[email protected]> Date: Sun Sep 15 10:51:48 2024 +0200 docs: add note on search udpates commit aa1b676 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 12:00:44 2024 +0200 docs: drop asciinema of package --init Signed-off-by:t Gerit Wagner <[email protected]> commit e791cc5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 09:41:21 2024 +0200 crossref: update printout commit ffd9628 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 14:02:14 2024 +0200 Reduce dependencies and switch to pydantic (#551) * move dependencies to arxiv and dedupe * pin numpy<2.0 * add bib-dedupe * switch to pydantic * switch to pydantic * update * sources. use relative filenames * update docs * fix mypy commit 1b84a37 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 10:13:18 2024 +0200 do not build paper in silent mode commit 910dffa Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:21 2024 +0200 add todo commit 7277c71 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:10 2024 +0200 fix import error: local_index.builder commit 026df75 Author: Gerit Wagner <[email protected]> Date: Wed Sep 11 07:09:15 2024 +0200 paper_md: stop container commit dc6ed46 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 11 06:19:15 2024 +0200 update dependencies (#550) Co-authored-by: Poetry updater <[email protected]> commit a4d12ec Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 20:40:56 2024 +0200 package_manager: packages do not necessarily start with "colrev." commit 5d23d21 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:36:08 2024 +0200 docker tests: remove intermediate containers commit 5142f4d Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:09:21 2024 +0200 docs: update path commit 2d6c2c2 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:08:34 2024 +0200 fix docker test commit 8c8f137 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 13:42:36 2024 +0200 docs: fix path commit 7b8c31e Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 09:23:19 2024 +0200 colrev project installation (making internal packages optional) (#530) * colrev project installation / make internal packages optional * drop optional extras from colrev * update * update gh-workflow Signed-off-by: Gerit Wagner <[email protected]> * format and docs * update upgrade * extract colrev-internal-package discovery * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * install packages after --add and init * add note on colrev install . to docs --------- Signed-off-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit bea78ac Author: Julian Prester <[email protected]> Date: Tue Sep 10 16:42:30 2024 +1000 Use posix paths for platform independence (#544) * Convert all paths for docker to posix * PRISMA: as_posix() * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * OCRMyPDF: as_posix() * fix prisma: path unlink() --------- Co-authored-by: Julian Prester <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> commit cd944e1 Author: Gerit Wagner <[email protected]> Date: Mon Sep 9 09:19:49 2024 +0200 europe_pmc: catch ValueError in lock.release() commit 685260b Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun Sep 8 14:44:24 2024 +0200 Update documentation (#548) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 046c09a Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:40 2024 +0200 Run Update documentation weekly to avoid many PRs commit 8fcb7e3 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:15 2024 +0200 refactor: pylint messages commit 3ea50f6 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:21:37 2024 +0200 crossref: catch Exception commit 163b5e1 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:19:55 2024 +0200 Update README.md commit 8f2460e Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:12:58 2024 +0200 update and rename workflows Signed-off-by: Gerit Wagner <[email protected]> commit c8bafc8 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:26:07 2024 +0200 data endpoint. add and commit commit b460db7 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:25:48 2024 +0200 init: check Docker available commit 85ea667 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 4 08:58:41 2024 +0200 update dependencies (#539) Co-authored-by: Poetry updater <[email protected]> commit 69d3eff Author: Gerit Wagner <[email protected]> Date: Wed Sep 4 07:41:42 2024 +0200 update relink_pdfs Signed-off-by: Gerit Wagner <[email protected]> commit fbd4d78 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 09:11:58 2024 +0200 add note on the order of pre/screening packages commit 09aa217 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 08:20:41 2024 +0200 update pdf text extraction commit 6588b68 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:26:21 2024 +0200 europe_pmc: refactor commit 9877da0 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:25:31 2024 +0200 crossref: refactor commit 7ba35df Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:35 2024 +0200 update print output commit dad30ad Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:05 2024 +0200 RecordNotInIndexException: ID mandatory commit 45deaa8 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:44 2024 +0200 pdf-get: fix symlinks after renamed dirs commit 91d5552 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:25 2024 +0200 load: warn on non-standardized fields (instead of raising exception) commit 829e036 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:20:57 2024 +0200 paper_md: fix path commit 5b4079e Author: Gerit Wagner <[email protected]> Date: Sat Aug 31 18:59:57 2024 +0200 sort SearchTypes commit 84d7901 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat Aug 31 16:20:02 2024 +0200 Update documentation (#528) Co-authored-by: github-actions <[email protected]>

Co-authored-by: Poetry updater <[email protected]>

* has_fatal_quality_defects() * create package ref_check * record_test: ignore mypy errors * add ref_check as a default package * remove record notes * reorder imports * update validation * update poetry.lock * sync with main commit 520a713 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:28:13 2024 +0200 fixes commit 227bf71 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:21:47 2024 +0200 record.change_entrytype(): run_quality_model() with set_prepared=True commit ba6ba8b Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:19:14 2024 +0200 record.remove_field_provenance_note(): also remove IGNORE:note commit 9f1c228 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:37 2024 +0200 no name-format defect for abbreviated names commit 8df75d4 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:02 2024 +0200 fix long line commit bbe831d Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:17:47 2024 +0200 update validation commit 12beaf5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:03:27 2024 +0200 update sync Signed-off-by: Gerit Wagner <[email protected]> commit 520192c Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:01:14 2024 +0200 update set_prepared in record.run_quality_model() commit ae108e5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:00:42 2024 +0200 crossref: raise ServiceNotAvailableException in crossref_query() commit 9d882f3 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 15:58:17 2024 +0200 prep polish: reset original state commit ddea08f Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:49 2024 +0200 [pre-commit.ci] pre-commit autoupdate (#556) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.7](astral-sh/ruff-pre-commit@v0.6.2...v0.6.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 77c055e Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:39 2024 +0200 update dependencies (#553) Co-authored-by: Poetry updater <[email protected]> commit d045a1d Author: Gerit Wagner <[email protected]> Date: Mon Sep 23 08:35:53 2024 +0200 fixes commit a112c20 Author: Carlo <[email protected]> Date: Fri Sep 20 07:38:10 2024 +0200 add command how to verify git credentials commit 81ebfb4 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 19:25:34 2024 +0200 move packages asciinema to comments commit 700c805 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 07:50:11 2024 +0200 testing/fixes commit 2605661 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 06:21:49 2024 +0200 tei_parser: set defaults commit cd42141 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:24:19 2024 +0200 upgrade: fix path-names in registry commit 36bfd05 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:08:04 2024 +0200 cli: add instructions commit ecbad8f Author: Gerit Wagner <[email protected]> Date: Sun Sep 15 10:51:48 2024 +0200 docs: add note on search udpates commit aa1b676 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 12:00:44 2024 +0200 docs: drop asciinema of package --init Signed-off-by:t Gerit Wagner <[email protected]> commit e791cc5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 09:41:21 2024 +0200 crossref: update printout commit ffd9628 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 14:02:14 2024 +0200 Reduce dependencies and switch to pydantic (#551) * move dependencies to arxiv and dedupe * pin numpy<2.0 * add bib-dedupe * switch to pydantic * switch to pydantic * update * sources. use relative filenames * update docs * fix mypy commit 1b84a37 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 10:13:18 2024 +0200 do not build paper in silent mode commit 910dffa Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:21 2024 +0200 add todo commit 7277c71 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:10 2024 +0200 fix import error: local_index.builder commit 026df75 Author: Gerit Wagner <[email protected]> Date: Wed Sep 11 07:09:15 2024 +0200 paper_md: stop container commit dc6ed46 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 11 06:19:15 2024 +0200 update dependencies (#550) Co-authored-by: Poetry updater <[email protected]> commit a4d12ec Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 20:40:56 2024 +0200 package_manager: packages do not necessarily start with "colrev." commit 5d23d21 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:36:08 2024 +0200 docker tests: remove intermediate containers commit 5142f4d Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:09:21 2024 +0200 docs: update path commit 2d6c2c2 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:08:34 2024 +0200 fix docker test commit 8c8f137 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 13:42:36 2024 +0200 docs: fix path commit 7b8c31e Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 09:23:19 2024 +0200 colrev project installation (making internal packages optional) (#530) * colrev project installation / make internal packages optional * drop optional extras from colrev * update * update gh-workflow Signed-off-by: Gerit Wagner <[email protected]> * format and docs * update upgrade * extract colrev-internal-package discovery * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * install packages after --add and init * add note on colrev install . to docs --------- Signed-off-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit bea78ac Author: Julian Prester <[email protected]> Date: Tue Sep 10 16:42:30 2024 +1000 Use posix paths for platform independence (#544) * Convert all paths for docker to posix * PRISMA: as_posix() * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * OCRMyPDF: as_posix() * fix prisma: path unlink() --------- Co-authored-by: Julian Prester <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> commit cd944e1 Author: Gerit Wagner <[email protected]> Date: Mon Sep 9 09:19:49 2024 +0200 europe_pmc: catch ValueError in lock.release() commit 685260b Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun Sep 8 14:44:24 2024 +0200 Update documentation (#548) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 046c09a Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:40 2024 +0200 Run Update documentation weekly to avoid many PRs commit 8fcb7e3 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:15 2024 +0200 refactor: pylint messages commit 3ea50f6 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:21:37 2024 +0200 crossref: catch Exception commit 163b5e1 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:19:55 2024 +0200 Update README.md commit 8f2460e Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:12:58 2024 +0200 update and rename workflows Signed-off-by: Gerit Wagner <[email protected]> commit c8bafc8 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:26:07 2024 +0200 data endpoint. add and commit commit b460db7 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:25:48 2024 +0200 init: check Docker available commit 85ea667 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 4 08:58:41 2024 +0200 update dependencies (#539) Co-authored-by: Poetry updater <[email protected]> commit 69d3eff Author: Gerit Wagner <[email protected]> Date: Wed Sep 4 07:41:42 2024 +0200 update relink_pdfs Signed-off-by: Gerit Wagner <[email protected]> commit fbd4d78 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 09:11:58 2024 +0200 add note on the order of pre/screening packages commit 09aa217 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 08:20:41 2024 +0200 update pdf text extraction commit 6588b68 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:26:21 2024 +0200 europe_pmc: refactor commit 9877da0 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:25:31 2024 +0200 crossref: refactor commit 7ba35df Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:35 2024 +0200 update print output commit dad30ad Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:05 2024 +0200 RecordNotInIndexException: ID mandatory commit 45deaa8 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:44 2024 +0200 pdf-get: fix symlinks after renamed dirs commit 91d5552 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:25 2024 +0200 load: warn on non-standardized fields (instead of raising exception) commit 829e036 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:20:57 2024 +0200 paper_md: fix path commit 5b4079e Author: Gerit Wagner <[email protected]> Date: Sat Aug 31 18:59:57 2024 +0200 sort SearchTypes commit 84d7901 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat Aug 31 16:20:02 2024 +0200 Update documentation (#528) Co-authored-by: github-actions <[email protected]> * add instruction to cli-validation * files_dir: stricter quality control * merge main commit d9a1a8a Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:33:22 2024 +0200 fix arxiv: pyproject.tomlÄ commit 38552d1 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:33:06 2024 +0200 fix naming conventions commit 6831e5b Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:07:16 2024 +0200 fix naming conventions commit a4aefd0 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:00:42 2024 +0200 install all-internal-packages for devcontainer (pylint) commit 5323329 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:57:18 2024 +0200 temporarily remove genai commit 520a713 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:28:13 2024 +0200 fixes commit 227bf71 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:21:47 2024 +0200 record.change_entrytype(): run_quality_model() with set_prepared=True commit ba6ba8b Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:19:14 2024 +0200 record.remove_field_provenance_note(): also remove IGNORE:note commit 9f1c228 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:37 2024 +0200 no name-format defect for abbreviated names commit 8df75d4 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:02 2024 +0200 fix long line commit bbe831d Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:17:47 2024 +0200 update validation commit 12beaf5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:03:27 2024 +0200 update sync Signed-off-by: Gerit Wagner <[email protected]> commit 520192c Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:01:14 2024 +0200 update set_prepared in record.run_quality_model() commit ae108e5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:00:42 2024 +0200 crossref: raise ServiceNotAvailableException in crossref_query() commit 9d882f3 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 15:58:17 2024 +0200 prep polish: reset original state commit ddea08f Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:49 2024 +0200 [pre-commit.ci] pre-commit autoupdate (#556) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.7](astral-sh/ruff-pre-commit@v0.6.2...v0.6.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 77c055e Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:39 2024 +0200 update dependencies (#553) Co-authored-by: Poetry updater <[email protected]> commit d045a1d Author: Gerit Wagner <[email protected]> Date: Mon Sep 23 08:35:53 2024 +0200 fixes commit a112c20 Author: Carlo <[email protected]> Date: Fri Sep 20 07:38:10 2024 +0200 add command how to verify git credentials commit 81ebfb4 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 19:25:34 2024 +0200 move packages asciinema to comments commit 700c805 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 07:50:11 2024 +0200 testing/fixes commit 2605661 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 06:21:49 2024 +0200 tei_parser: set defaults commit cd42141 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:24:19 2024 +0200 upgrade: fix path-names in registry commit 36bfd05 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:08:04 2024 +0200 cli: add instructions commit ecbad8f Author: Gerit Wagner <[email protected]> Date: Sun Sep 15 10:51:48 2024 +0200 docs: add note on search udpates commit aa1b676 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 12:00:44 2024 +0200 docs: drop asciinema of package --init Signed-off-by:t Gerit Wagner <[email protected]> commit e791cc5 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 09:41:21 2024 +0200 crossref: update printout commit ffd9628 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 14:02:14 2024 +0200 Reduce dependencies and switch to pydantic (#551) * move dependencies to arxiv and dedupe * pin numpy<2.0 * add bib-dedupe * switch to pydantic * switch to pydantic * update * sources. use relative filenames * update docs * fix mypy commit 1b84a37 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 10:13:18 2024 +0200 do not build paper in silent mode commit 910dffa Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:21 2024 +0200 add todo commit 7277c71 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:10 2024 +0200 fix import error: local_index.builder commit 026df75 Author: Gerit Wagner <[email protected]> Date: Wed Sep 11 07:09:15 2024 +0200 paper_md: stop container commit dc6ed46 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 11 06:19:15 2024 +0200 update dependencies (#550) Co-authored-by: Poetry updater <[email protected]> commit a4d12ec Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 20:40:56 2024 +0200 package_manager: packages do not necessarily start with "colrev." commit 5d23d21 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:36:08 2024 +0200 docker tests: remove intermediate containers commit 5142f4d Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:09:21 2024 +0200 docs: update path commit 2d6c2c2 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:08:34 2024 +0200 fix docker test commit 8c8f137 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 13:42:36 2024 +0200 docs: fix path commit 7b8c31e Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 09:23:19 2024 +0200 colrev project installation (making internal packages optional) (#530) * colrev project installation / make internal packages optional * drop optional extras from colrev * update * update gh-workflow Signed-off-by: Gerit Wagner <[email protected]> * format and docs * update upgrade * extract colrev-internal-package discovery * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * install packages after --add and init * add note on colrev install . to docs --------- Signed-off-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit bea78ac Author: Julian Prester <[email protected]> Date: Tue Sep 10 16:42:30 2024 +1000 Use posix paths for platform independence (#544) * Convert all paths for docker to posix * PRISMA: as_posix() * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * OCRMyPDF: as_posix() * fix prisma: path unlink() --------- Co-authored-by: Julian Prester <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> commit cd944e1 Author: Gerit Wagner <[email protected]> Date: Mon Sep 9 09:19:49 2024 +0200 europe_pmc: catch ValueError in lock.release() commit 685260b Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun Sep 8 14:44:24 2024 +0200 Update documentation (#548) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 046c09a Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:40 2024 +0200 Run Update documentation weekly to avoid many PRs commit 8fcb7e3 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:15 2024 +0200 refactor: pylint messages commit 3ea50f6 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:21:37 2024 +0200 crossref: catch Exception commit 163b5e1 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:19:55 2024 +0200 Update README.md commit 8f2460e Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:12:58 2024 +0200 update and rename workflows Signed-off-by: Gerit Wagner <[email protected]> commit c8bafc8 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:26:07 2024 +0200 data endpoint. add and commit commit b460db7 Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:25:48 2024 +0200 init: check Docker available commit 85ea667 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 4 08:58:41 2024 +0200 update dependencies (#539) Co-authored-by: Poetry updater <[email protected]> commit 69d3eff Author: Gerit Wagner <[email protected]> Date: Wed Sep 4 07:41:42 2024 +0200 update relink_pdfs Signed-off-by: Gerit Wagner <[email protected]> commit fbd4d78 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 09:11:58 2024 +0200 add note on the order of pre/screening packages commit 09aa217 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 08:20:41 2024 +0200 update pdf text extraction commit 6588b68 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:26:21 2024 +0200 europe_pmc: refactor commit 9877da0 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:25:31 2024 +0200 crossref: refactor commit 7ba35df Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:35 2024 +0200 update print output commit dad30ad Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:05 2024 +0200 RecordNotInIndexException: ID mandatory commit 45deaa8 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:44 2024 +0200 pdf-get: fix symlinks after renamed dirs commit 91d5552 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:25 2024 +0200 load: warn on non-standardized fields (instead of raising exception) commit 829e036 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:20:57 2024 +0200 paper_md: fix path commit 5b4079e Author: Gerit Wagner <[email protected]> Date: Sat Aug 31 18:59:57 2024 +0200 sort SearchTypes commit 84d7901 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat Aug 31 16:20:02 2024 +0200 Update documentation (#528) Co-authored-by: github-actions <[email protected]>

* Move prescreen inclusion criterion input to ops prescreen * update and rename workflows Signed-off-by: Gerit Wagner <[email protected]> * Update README.md * crossref: catch Exception * refactor: pylint messages * Run Update documentation weekly to avoid many PRs * Update documentation (#548) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * europe_pmc: catch ValueError in lock.release() * Use posix paths for platform independence (#544) * Convert all paths for docker to posix * PRISMA: as_posix() * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * OCRMyPDF: as_posix() * fix prisma: path unlink() --------- Co-authored-by: Julian Prester <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> * colrev project installation (making internal packages optional) (#530) * colrev project installation / make internal packages optional * drop optional extras from colrev * update * update gh-workflow Signed-off-by: Gerit Wagner <[email protected]> * format and docs * update upgrade * extract colrev-internal-package discovery * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * install packages after --add and init * add note on colrev install . to docs --------- Signed-off-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * docs: fix path * fix docker test * docs: update path * docker tests: remove intermediate containers * package_manager: packages do not necessarily start with "colrev." * update dependencies (#550) Co-authored-by: Poetry updater <[email protected]> * paper_md: stop container * fix import error: local_index.builder * add todo * do not build paper in silent mode * Reduce dependencies and switch to pydantic (#551) * move dependencies to arxiv and dedupe * pin numpy<2.0 * add bib-dedupe * switch to pydantic * switch to pydantic * update * sources. use relative filenames * update docs * fix mypy * crossref: update printout * docs: drop asciinema of package --init Signed-off-by:t Gerit Wagner <[email protected]> * docs: add note on search udpates * cli: add instructions * upgrade: fix path-names in registry * tei_parser: set defaults * testing/fixes * Export instead of print * Remove instructor dependency * Split prompt into system and user * align screening output with prescreen file export * move packages asciinema to comments * add command how to verify git credentials * fixes * update dependencies (#553) Co-authored-by: Poetry updater <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#556) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.2...v0.6.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * prep polish: reset original state * crossref: raise ServiceNotAvailableException in crossref_query() * update set_prepared in record.run_quality_model() * update sync Signed-off-by: Gerit Wagner <[email protected]> * update validation * fix long line * no name-format defect for abbreviated names * record.remove_field_provenance_note(): also remove IGNORE:note * record.change_entrytype(): run_quality_model() with set_prepared=True * fixes * temporarily remove genai * install all-internal-packages for devcontainer (pylint) * fix naming conventions * fix naming conventions * fix arxiv: pyproject.toml * Relax prep (#529) * has_fatal_quality_defects() * create package ref_check * record_test: ignore mypy errors * add ref_check as a default package * remove record notes * reorder imports * update validation * update poetry.lock * sync with main commit 520a71356c5767cfba5a133e788826680d70377d Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:28:13 2024 +0200 fixes commit 227bf715ae4c39b88d4fceb20353d6cac3787c7a Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:21:47 2024 +0200 record.change_entrytype(): run_quality_model() with set_prepared=True commit ba6ba8be481266c12cb6d0551ad08e4ea34b98ce Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:19:14 2024 +0200 record.remove_field_provenance_note(): also remove IGNORE:note commit 9f1c22814d5d34bfa7cf03b90b39d71e961ec597 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:37 2024 +0200 no name-format defect for abbreviated names commit 8df75d4dc2f846eda85ce4589b4a0388cacde0f0 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:02 2024 +0200 fix long line commit bbe831ddbc141da318c2c356a2f4b1ff61a31825 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:17:47 2024 +0200 update validation commit 12beaf5fdd4d874bc798d229896498850060da5a Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:03:27 2024 +0200 update sync Signed-off-by: Gerit Wagner <[email protected]> commit 520192c39ea21904d828fa6c4d863a5859c1a2d9 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:01:14 2024 +0200 update set_prepared in record.run_quality_model() commit ae108e57f14be0d20c4a275b40ed470457b1e262 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:00:42 2024 +0200 crossref: raise ServiceNotAvailableException in crossref_query() commit 9d882f338fb47a9fb200b98130c6504b46ef7709 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 15:58:17 2024 +0200 prep polish: reset original state commit ddea08ff0f0ffe79a2b40e560548f5ea9d1709c3 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:49 2024 +0200 [pre-commit.ci] pre-commit autoupdate (#556) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.2...v0.6.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 77c055e610f179fc76a0006f5ad11391d979111b Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:39 2024 +0200 update dependencies (#553) Co-authored-by: Poetry updater <[email protected]> commit d045a1da20b5dac6562aac34668c58666fb90e5b Author: Gerit Wagner <[email protected]> Date: Mon Sep 23 08:35:53 2024 +0200 fixes commit a112c204f219ad180f2471126fd685efa0f66a6d Author: Carlo <[email protected]> Date: Fri Sep 20 07:38:10 2024 +0200 add command how to verify git credentials commit 81ebfb4c6c2202191b28c9bb590dbf79509d30f8 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 19:25:34 2024 +0200 move packages asciinema to comments commit 700c80508455046f2407aa493b36ba2760ccbed1 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 07:50:11 2024 +0200 testing/fixes commit 260566119990226e07a1485bbead1c73900560a8 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 06:21:49 2024 +0200 tei_parser: set defaults commit cd4214116c90e70c369edb38eb3a2e8999a97b29 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:24:19 2024 +0200 upgrade: fix path-names in registry commit 36bfd051989681c992b4743963df1a5053924884 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:08:04 2024 +0200 cli: add instructions commit ecbad8fc09c548ff1e9507269b6bc09a2ce26769 Author: Gerit Wagner <[email protected]> Date: Sun Sep 15 10:51:48 2024 +0200 docs: add note on search udpates commit aa1b6766a03a02151c4838422995bc7fe2581374 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 12:00:44 2024 +0200 docs: drop asciinema of package --init Signed-off-by:t Gerit Wagner <[email protected]> commit e791cc50bc8fd25ef209e3bef77342f31efe4e6f Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 09:41:21 2024 +0200 crossref: update printout commit ffd96287d953fd440dc26380ea3117ad32ce47ee Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 14:02:14 2024 +0200 Reduce dependencies and switch to pydantic (#551) * move dependencies to arxiv and dedupe * pin numpy<2.0 * add bib-dedupe * switch to pydantic * switch to pydantic * update * sources. use relative filenames * update docs * fix mypy commit 1b84a37edd4767c96d46f17e765aa1d98a99a9d8 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 10:13:18 2024 +0200 do not build paper in silent mode commit 910dffac5f95df8e02b0efaf11c0a017de306f78 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:21 2024 +0200 add todo commit 7277c719f08c49274724ceb0f4af0b14c906f189 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:10 2024 +0200 fix import error: local_index.builder commit 026df759a150167b472fdd554683b8b491eb8105 Author: Gerit Wagner <[email protected]> Date: Wed Sep 11 07:09:15 2024 +0200 paper_md: stop container commit dc6ed4676acaf5a17eb9f5e8024a0ab848ae455a Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 11 06:19:15 2024 +0200 update dependencies (#550) Co-authored-by: Poetry updater <[email protected]> commit a4d12eccffc938a5c91ab117cf35e24120f45965 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 20:40:56 2024 +0200 package_manager: packages do not necessarily start with "colrev." commit 5d23d210d85c3ff0e16ae274d28690f0019e87d1 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:36:08 2024 +0200 docker tests: remove intermediate containers commit 5142f4db641252e2bd667752cf3a9d7ae54e7cfa Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:09:21 2024 +0200 docs: update path commit 2d6c2c28bcb803b7777adc0be79e41e665af05fe Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:08:34 2024 +0200 fix docker test commit 8c8f1370abf2dcbb5ab659c658f4411d46250425 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 13:42:36 2024 +0200 docs: fix path commit 7b8c31ed98f2b8e104b5f6e942e90f951160b280 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 09:23:19 2024 +0200 colrev project installation (making internal packages optional) (#530) * colrev project installation / make internal packages optional * drop optional extras from colrev * update * update gh-workflow Signed-off-by: Gerit Wagner <[email protected]> * format and docs * update upgrade * extract colrev-internal-package discovery * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * install packages after --add and init * add note on colrev install . to docs --------- Signed-off-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit bea78ac507f362feb3b6126d01342a0d7f61ebec Author: Julian Prester <[email protected]> Date: Tue Sep 10 16:42:30 2024 +1000 Use posix paths for platform independence (#544) * Convert all paths for docker to posix * PRISMA: as_posix() * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * OCRMyPDF: as_posix() * fix prisma: path unlink() --------- Co-authored-by: Julian Prester <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> commit cd944e1db31a4365a225672f7b082be95db5efef Author: Gerit Wagner <[email protected]> Date: Mon Sep 9 09:19:49 2024 +0200 europe_pmc: catch ValueError in lock.release() commit 685260be988edbb47d725cbfac298075ab46e011 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun Sep 8 14:44:24 2024 +0200 Update documentation (#548) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 046c09ae0ff7f9a8f910e90a03c5585295797469 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:40 2024 +0200 Run Update documentation weekly to avoid many PRs commit 8fcb7e347ba1e29f26785d682e5c346be91a5237 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:15 2024 +0200 refactor: pylint messages commit 3ea50f6a377989081a06752a5a76492763385975 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:21:37 2024 +0200 crossref: catch Exception commit 163b5e10d88399fa88998ac04d63578e37dd51e3 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:19:55 2024 +0200 Update README.md commit 8f2460eb54e931d82d6b680107f05fd7736ff5a1 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:12:58 2024 +0200 update and rename workflows Signed-off-by: Gerit Wagner <[email protected]> commit c8bafc81c457e6007d33eb85635998eceec534bf Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:26:07 2024 +0200 data endpoint. add and commit commit b460db7230858c9cced3592e7d8c2ed759e437ec Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:25:48 2024 +0200 init: check Docker available commit 85ea667aa9571a118ef6688e86a78e64d77f0641 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 4 08:58:41 2024 +0200 update dependencies (#539) Co-authored-by: Poetry updater <[email protected]> commit 69d3eff5daf2df1a37816fc062eae73e6c11eecd Author: Gerit Wagner <[email protected]> Date: Wed Sep 4 07:41:42 2024 +0200 update relink_pdfs Signed-off-by: Gerit Wagner <[email protected]> commit fbd4d780c275fbdf04e409a3d7f0c70843f400e2 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 09:11:58 2024 +0200 add note on the order of pre/screening packages commit 09aa2173829f03b177c60f38b76acf4fcc5d8649 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 08:20:41 2024 +0200 update pdf text extraction commit 6588b6867806312c24bb3bfd7d6eb0fc80860747 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:26:21 2024 +0200 europe_pmc: refactor commit 9877da003ef1085b4222c1d17bc0d364a00161c2 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:25:31 2024 +0200 crossref: refactor commit 7ba35df3e0ecfe204b3c639fd062e086a06e080d Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:35 2024 +0200 update print output commit dad30adb357ac0f38c171d1a5b9997e3a275e576 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:05 2024 +0200 RecordNotInIndexException: ID mandatory commit 45deaa89b222308c093505af150a392b97868db7 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:44 2024 +0200 pdf-get: fix symlinks after renamed dirs commit 91d5552929b026d1cd6fb0fe9bf11bf716b8a698 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:25 2024 +0200 load: warn on non-standardized fields (instead of raising exception) commit 829e036c061b1fc2903785500387924894525ff4 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:20:57 2024 +0200 paper_md: fix path commit 5b4079e6cc0a66877a0f82c15d9683a65632423e Author: Gerit Wagner <[email protected]> Date: Sat Aug 31 18:59:57 2024 +0200 sort SearchTypes commit 84d7901208ed067e40443f2ec55bfd5a3a712a8f Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat Aug 31 16:20:02 2024 +0200 Update documentation (#528) Co-authored-by: github-actions <[email protected]> * add instruction to cli-validation * files_dir: stricter quality control * merge main commit d9a1a8a4c5377e63846390e2a63f7bbe0bc18c5e Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:33:22 2024 +0200 fix arxiv: pyproject.tomlÄ commit 38552d1e5ad970d094d87c35b42f1f661d084ed1 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:33:06 2024 +0200 fix naming conventions commit 6831e5b65d4b608056ecab0ae428897d0eddd9b7 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:07:16 2024 +0200 fix naming conventions commit a4aefd01ebcd9365336e78c6efba34fe3426bf32 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 17:00:42 2024 +0200 install all-internal-packages for devcontainer (pylint) commit 532332997178ab99bc23c78e22dbf0acb27f425d Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:57:18 2024 +0200 temporarily remove genai commit 520a71356c5767cfba5a133e788826680d70377d Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:28:13 2024 +0200 fixes commit 227bf715ae4c39b88d4fceb20353d6cac3787c7a Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:21:47 2024 +0200 record.change_entrytype(): run_quality_model() with set_prepared=True commit ba6ba8be481266c12cb6d0551ad08e4ea34b98ce Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:19:14 2024 +0200 record.remove_field_provenance_note(): also remove IGNORE:note commit 9f1c22814d5d34bfa7cf03b90b39d71e961ec597 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:37 2024 +0200 no name-format defect for abbreviated names commit 8df75d4dc2f846eda85ce4589b4a0388cacde0f0 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:18:02 2024 +0200 fix long line commit bbe831ddbc141da318c2c356a2f4b1ff61a31825 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:17:47 2024 +0200 update validation commit 12beaf5fdd4d874bc798d229896498850060da5a Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:03:27 2024 +0200 update sync Signed-off-by: Gerit Wagner <[email protected]> commit 520192c39ea21904d828fa6c4d863a5859c1a2d9 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:01:14 2024 +0200 update set_prepared in record.run_quality_model() commit ae108e57f14be0d20c4a275b40ed470457b1e262 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 16:00:42 2024 +0200 crossref: raise ServiceNotAvailableException in crossref_query() commit 9d882f338fb47a9fb200b98130c6504b46ef7709 Author: Gerit Wagner <[email protected]> Date: Sat Sep 28 15:58:17 2024 +0200 prep polish: reset original state commit ddea08ff0f0ffe79a2b40e560548f5ea9d1709c3 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:49 2024 +0200 [pre-commit.ci] pre-commit autoupdate (#556) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.2...v0.6.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 77c055e610f179fc76a0006f5ad11391d979111b Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue Sep 24 06:16:39 2024 +0200 update dependencies (#553) Co-authored-by: Poetry updater <[email protected]> commit d045a1da20b5dac6562aac34668c58666fb90e5b Author: Gerit Wagner <[email protected]> Date: Mon Sep 23 08:35:53 2024 +0200 fixes commit a112c204f219ad180f2471126fd685efa0f66a6d Author: Carlo <[email protected]> Date: Fri Sep 20 07:38:10 2024 +0200 add command how to verify git credentials commit 81ebfb4c6c2202191b28c9bb590dbf79509d30f8 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 19:25:34 2024 +0200 move packages asciinema to comments commit 700c80508455046f2407aa493b36ba2760ccbed1 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 07:50:11 2024 +0200 testing/fixes commit 260566119990226e07a1485bbead1c73900560a8 Author: Gerit Wagner <[email protected]> Date: Thu Sep 19 06:21:49 2024 +0200 tei_parser: set defaults commit cd4214116c90e70c369edb38eb3a2e8999a97b29 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:24:19 2024 +0200 upgrade: fix path-names in registry commit 36bfd051989681c992b4743963df1a5053924884 Author: Gerit Wagner <[email protected]> Date: Mon Sep 16 11:08:04 2024 +0200 cli: add instructions commit ecbad8fc09c548ff1e9507269b6bc09a2ce26769 Author: Gerit Wagner <[email protected]> Date: Sun Sep 15 10:51:48 2024 +0200 docs: add note on search udpates commit aa1b6766a03a02151c4838422995bc7fe2581374 Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 12:00:44 2024 +0200 docs: drop asciinema of package --init Signed-off-by:t Gerit Wagner <[email protected]> commit e791cc50bc8fd25ef209e3bef77342f31efe4e6f Author: Gerit Wagner <[email protected]> Date: Sat Sep 14 09:41:21 2024 +0200 crossref: update printout commit ffd96287d953fd440dc26380ea3117ad32ce47ee Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 14:02:14 2024 +0200 Reduce dependencies and switch to pydantic (#551) * move dependencies to arxiv and dedupe * pin numpy<2.0 * add bib-dedupe * switch to pydantic * switch to pydantic * update * sources. use relative filenames * update docs * fix mypy commit 1b84a37edd4767c96d46f17e765aa1d98a99a9d8 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 10:13:18 2024 +0200 do not build paper in silent mode commit 910dffac5f95df8e02b0efaf11c0a017de306f78 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:21 2024 +0200 add todo commit 7277c719f08c49274724ceb0f4af0b14c906f189 Author: Gerit Wagner <[email protected]> Date: Fri Sep 13 08:05:10 2024 +0200 fix import error: local_index.builder commit 026df759a150167b472fdd554683b8b491eb8105 Author: Gerit Wagner <[email protected]> Date: Wed Sep 11 07:09:15 2024 +0200 paper_md: stop container commit dc6ed4676acaf5a17eb9f5e8024a0ab848ae455a Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 11 06:19:15 2024 +0200 update dependencies (#550) Co-authored-by: Poetry updater <[email protected]> commit a4d12eccffc938a5c91ab117cf35e24120f45965 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 20:40:56 2024 +0200 package_manager: packages do not necessarily start with "colrev." commit 5d23d210d85c3ff0e16ae274d28690f0019e87d1 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:36:08 2024 +0200 docker tests: remove intermediate containers commit 5142f4db641252e2bd667752cf3a9d7ae54e7cfa Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:09:21 2024 +0200 docs: update path commit 2d6c2c28bcb803b7777adc0be79e41e665af05fe Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 14:08:34 2024 +0200 fix docker test commit 8c8f1370abf2dcbb5ab659c658f4411d46250425 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 13:42:36 2024 +0200 docs: fix path commit 7b8c31ed98f2b8e104b5f6e942e90f951160b280 Author: Gerit Wagner <[email protected]> Date: Tue Sep 10 09:23:19 2024 +0200 colrev project installation (making internal packages optional) (#530) * colrev project installation / make internal packages optional * drop optional extras from colrev * update * update gh-workflow Signed-off-by: Gerit Wagner <[email protected]> * format and docs * update upgrade * extract colrev-internal-package discovery * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * install packages after --add and init * add note on colrev install . to docs --------- Signed-off-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit bea78ac507f362feb3b6126d01342a0d7f61ebec Author: Julian Prester <[email protected]> Date: Tue Sep 10 16:42:30 2024 +1000 Use posix paths for platform independence (#544) * Convert all paths for docker to posix * PRISMA: as_posix() * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * OCRMyPDF: as_posix() * fix prisma: path unlink() --------- Co-authored-by: Julian Prester <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> commit cd944e1db31a4365a225672f7b082be95db5efef Author: Gerit Wagner <[email protected]> Date: Mon Sep 9 09:19:49 2024 +0200 europe_pmc: catch ValueError in lock.release() commit 685260be988edbb47d725cbfac298075ab46e011 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun Sep 8 14:44:24 2024 +0200 Update documentation (#548) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 046c09ae0ff7f9a8f910e90a03c5585295797469 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:40 2024 +0200 Run Update documentation weekly to avoid many PRs commit 8fcb7e347ba1e29f26785d682e5c346be91a5237 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:52:15 2024 +0200 refactor: pylint messages commit 3ea50f6a377989081a06752a5a76492763385975 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:21:37 2024 +0200 crossref: catch Exception commit 163b5e10d88399fa88998ac04d63578e37dd51e3 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:19:55 2024 +0200 Update README.md commit 8f2460eb54e931d82d6b680107f05fd7736ff5a1 Author: Gerit Wagner <[email protected]> Date: Sun Sep 8 09:12:58 2024 +0200 update and rename workflows Signed-off-by: Gerit Wagner <[email protected]> commit c8bafc81c457e6007d33eb85635998eceec534bf Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:26:07 2024 +0200 data endpoint. add and commit commit b460db7230858c9cced3592e7d8c2ed759e437ec Author: Gerit Wagner <[email protected]> Date: Fri Sep 6 08:25:48 2024 +0200 init: check Docker available commit 85ea667aa9571a118ef6688e86a78e64d77f0641 Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed Sep 4 08:58:41 2024 +0200 update dependencies (#539) Co-authored-by: Poetry updater <[email protected]> commit 69d3eff5daf2df1a37816fc062eae73e6c11eecd Author: Gerit Wagner <[email protected]> Date: Wed Sep 4 07:41:42 2024 +0200 update relink_pdfs Signed-off-by: Gerit Wagner <[email protected]> commit fbd4d780c275fbdf04e409a3d7f0c70843f400e2 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 09:11:58 2024 +0200 add note on the order of pre/screening packages commit 09aa2173829f03b177c60f38b76acf4fcc5d8649 Author: Gerit Wagner <[email protected]> Date: Tue Sep 3 08:20:41 2024 +0200 update pdf text extraction commit 6588b6867806312c24bb3bfd7d6eb0fc80860747 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:26:21 2024 +0200 europe_pmc: refactor commit 9877da003ef1085b4222c1d17bc0d364a00161c2 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:25:31 2024 +0200 crossref: refactor commit 7ba35df3e0ecfe204b3c639fd062e086a06e080d Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:35 2024 +0200 update print output commit dad30adb357ac0f38c171d1a5b9997e3a275e576 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:24:05 2024 +0200 RecordNotInIndexException: ID mandatory commit 45deaa89b222308c093505af150a392b97868db7 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:44 2024 +0200 pdf-get: fix symlinks after renamed dirs commit 91d5552929b026d1cd6fb0fe9bf11bf716b8a698 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:22:25 2024 +0200 load: warn on non-standardized fields (instead of raising exception) commit 829e036c061b1fc2903785500387924894525ff4 Author: Gerit Wagner <[email protected]> Date: Mon Sep 2 18:20:57 2024 +0200 paper_md: fix path commit 5b4079e6cc0a66877a0f82c15d9683a65632423e Author: Gerit Wagner <[email protected]> Date: Sat Aug 31 18:59:57 2024 +0200 sort SearchTypes commit 84d7901208ed067e40443f2ec55bfd5a3a712a8f Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat Aug 31 16:20:02 2024 +0200 Update documentation (#528) Co-authored-by: github-actions <[email protected]> * update upgrade of gh-actions * doi_org: use re instead of bs4 * record.has_fatal_quality_defects(): catch doi/numbers Signed-off-by: Gerit Wagner <[email protected]> * update GROBID * fix tei_parser * search_api_feed: make _add_record_to_feed public and remove redundant _get_prev_feed_record * colrev.files_dir: update rerun * fix linter messages: colrev.files_dir * update grobid-0.8.1 tests * update dependencies (#560) Co-authored-by: Poetry updater <[email protected]> * Update documentation (#561) Co-authored-by: github-actions <[email protected]> * colrev.github: support topic field, use inquirer * update dependencies (#562) Co-authored-by: Poetry updater <[email protected]> * update links/docs * colrev.files_dir: catch exception * update docs * colrev.arxiv: fix feedparser dep * colrev.files_dir: ignore pylint * release 0.13.0 * update doi in CITATION.cff * colrev.files_dir: catch connection error * add comparison * update README.md * update overview * update readme * update comparison * update docs * update docs/index * udpate docs/index * colrev-packages: if direct-url does not start with file://, it is not local * colrev-packages: shallow clone * init: install package before instantiating * update overview * add python venv instructions to getting started page * install setuptools with --break-system-packages * drop click_completion, update zope.interface * fix pylint warnings * codespaces: py3.12 * colrev init: add not to install internal_packages * temporarily deactivate is_installed() * add "colrev install all-packages" to getting started install steps * fix previous wrong colrev package command * set python version for workflow/tests * fix pylint warnings * package-manager: import pypi packages containing colrev in package-name * add bs4 dependency for docs * update dependencies * deps: add mypy to dev * fix: package name validation * fix: do not call install() in init * feat: create two commits upon init allows users to see one commit with the settings and data packages separate from the commit with the general file setup (e.g., gitignore, LICENSE) * deps: update bib-dedupe and Python (3.10-3.12) - fixes vulnerability in setuptools Squashed commit of the following: commit 0001f84e84f6d874851b2e0936854b54bfd2057a Author: Gerit Wagner <[email protected]> Date: Tue Oct 22 15:52:28 2024 +0200 add note on Python3.13 commit c3e79f9112217beff85718ed1f6e3922831077d0 Author: Gerit Wagner <[email protected]> Date: Tue Oct 22 15:08:31 2024 +0200 tests: specify python version for pipx install poetry commit 9745ae0f4bb06a6081f03dd32a167677f99ba914 Author: Gerit Wagner <[email protected]> Date: Mon Oct 21 09:08:58 2024 +0200 tests: drop python 3.13. full test commit 306f023b7b64a5c60f1a83dd19fa4437cf8ac482 Author: Gerit Wagner <[email protected]> Date: Mon Oct 21 07:35:40 2024 +0200 deps: update lxml commit 0c0a3596371704809d12fd0ee6c1150651cf1005 Author: Gerit Wagner <[email protected]> Date: Mon Oct 21 06:52:57 2024 +0200 deps: update bib-dedupe (Python, numpy) * docs: reduce badges * add installation of diverse internal packages * restructure installation of CoLRev and pre-commit hooks * update * dev: remove setup.md from devcontainer * docs: fix typo * update dependencies * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.6.0...v5.0.0) - [github.com/psf/black-pre-commit-mirror: 24.8.0 → 24.10.0](https://github.com/psf/black-pre-commit-mirror/compare/24.8.0...24.10.0) - [github.com/asottile/reorder-python-imports: v3.13.0 → v3.14.0](https://github.com/asottile/reorder-python-imports/compare/v3.13.0...v3.14.0) - [github.com/asottile/pyupgrade: v3.17.0 → v3.19.0](https://github.com/asottile/pyupgrade/compare/v3.17.0...v3.19.0) - [github.com/pre-commit/mirrors-mypy: v1.11.2 → v1.13.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.11.2...v1.13.0) - [github.com/astral-sh/ruff-pre-commit: v0.6.7 → v0.7.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.7...v0.7.1) * deps: add importlib_metadata for dash * deps: poetry updates manually (not as a cronjob) * crossref,dblp: update formatting * docs: include colrev-scidb * docs: update colrev-scidb * Update documentation (#573) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update documentation (#575) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * fix: entering author details in package --init * ui: add note for colrev package --init * fix: crossref - use cursor method for large queries * rename test files * fix: package_manager init built-in * release 0.13.1 * docs: SearchSource * version: drop pre-python3.8 * crossref: add get_dois() * format * deps: update pre-commit to prevent InvalidManifest error * search: catch ModuleNotFound * update synergy-datasets * release 0.13.2 * update mypy-python version * deps: update to bib-dedupe (silenced pandas warnings) * fix: europe_pmc empty-list * update pre-commit hooks * remove pylint flags * synergy: extract method * crossref: rename attribute * update docs * extract colrev.sync to separate PyPI package * extract hooks-update to colrev-sync * docs: remove hooks.update * fix: scope-prescreen optional with None * add colrev convert (cli) * update gh-action workflows * gh-actions: update deploy * update record_id_setter (for colrev convert) * colrev.plos package (#594) * Package PLOS created * Creating SearchSource Plos * Update plos_search_source.py * Fixing upload of SearchSource Plos * Skeleton of package plos * Fixing pushing to git * A few errors fixed * Main branch update with run error fixed * Fixing push * Fixing push 2 * Created file record_transformer and sttarted method json_to_record * Implemented some methods for the json_to_record * Record_transformer_class * Get variables from PLOS result * merged other branch, record transformer class completed * Add _prep_plos_record method for PLOS record preparation * Implemented method scope_excluded * merge branches to present * Fixed errors during meeting * Added save line in run_api_search * The format of the numbers and authors has changed. The abstract needs to be reviewed. * load implemented * unit_test * Some errors fixed * Documentation. Fixed errors from unit_test. Fixed error YEAR * Inputs and prints removed * Merged prepare branch into this branch * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * First test passed. (review method _item_to_record) * Unit-Test completed * Deleted useless files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update format of publication_date filter * remove logging settings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fixed pre-commit warnings * Module search deleted * undo unrelated changes * undo change * remove article_type (not returned in item) * reinclude pylint/crossref * copy README for import to CoLRev docs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * drop TOC * remove prep endpoint * import colrev.plos into colrev docs * update contributors --------- Co-authored-by: julialopezmarti <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> * prospero searchsource (#586) * new branch prospero-serachsource created, prospero package initialised and installed * created python file for functionalities, defined class properties * trivial changes added to prospero.py * Add requirements.txt for dependency management * Add Selenium setup, test script, and ChromeDriver * Add working load and add_endpoint methods for ProsperoSearchSource * search_func extract meta data, not tested * expand search_func * add test file * extract the content from columns * add into search method amount of articles from prospero * add into search method amount of articles from prospero * Update Prospero search functionality and tests * allow user input for search bar * save records into bib file * Fix indexing issues and improve BibTeX export in Prospero search * change variable names for better clarity, driver navigates between pages * Update ProsperoSearchSource with improved load methods and configurations * seperate smaller methods for better clarity * updates files * Fix add_endpoint method in ProsperoSearchSource for unique filenames and API compatibility * add run_api_search method * change naming for better clarity * rearrange import block for better clarity * change file name for better clarity * add heuristic method * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small fixes and saving a basic bib file after blocks getting deleted! * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * load language, authors into bib file, fix repeated loading error * add run_api_search method * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * readjust page counter * add trivial changes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update prospero.py: Fixed KeyError, improved search functionality, and removed unwanted lines * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove source_identifier property * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * change year field * change prospero_status * add documentation in README file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update documentation * update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * poetry add selenium * add selenium dependencies * add search_parameters * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update search_parameters * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove bibtexparser dependency and rely on feed.save * added names of all members in toml file * Removed unnecessary files: .vscode/settings.json and requirements.txt * minimize console output, delete old test files * delete old selenium test files * Fix some flake8/mypy issues in ProsperoSearchSource * use review_manager.logger * fix several pylint issues * fix pylint * FIX None-Working Code * Fix: Resolve pre-commit warnings in prospero.py * add pylint disable * add pylint disable for prospero.py * Fix: Resolve pre-commit warnings in get_record_info.py * copy README for colrev docs * revise code * refactor * refactor: extract api module * update docs * move URL_PREFIX to class attribute * update contributors --------- Co-authored-by: ammar-uni <[email protected]> Co-authored-by: OlhaKomashevska <[email protected]> Co-authored-by: komashevska <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> * Update documentation (#603) * Update documentation * [pre-commit.ci] auto fixes from 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[github.com/psf/black-pre-commit-mirror: 24.10.0 → 25.1.0](https://github.com/psf/black-pre-commit-mirror/compare/24.10.0...25.1.0) - [github.com/asottile/pyupgrade: v3.19.0 → v3.19.1](https://github.com/asottile/pyupgrade/compare/v3.19.0...v3.19.1) - [github.com/pre-commit/mirrors-mypy: v1.13.0 → v1.15.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.13.0...v1.15.0) - [github.com/astral-sh/ruff-pre-commit: v0.7.1 → v0.9.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.1...v0.9.6) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * update docs * fix pylint warnings in cli * consistently update settings in add_package_to_settings * fix pylint warning in plos * update scope_prescreen and docs * docs: update files_dir * update docs * update cli handling * fix: loader accept empty fields * update * Replace 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update publishing workflow * fix pyproject.tomls/dependencies * release 0.14.0 * update doi, release checklist * update docs * update docs * update README/release-checklist * fix link * update nr extensions * update PLOS api/docs * update covert: ris * update ris writer * update load-utils: load_df * fixes * temporarily remove genai * Update documentation (#575) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Export instead of print * fixes * temporarily remove genai * Update documentation (#575) * Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update pyproject.toml * prescreen: use input() in package instead of operation * fix * fix * fix * switch from zope-interface to ABC * udpate package * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Signed-off-by: Gerit Wagner <[email protected]> Co-authored-by: Julian Prester <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: Gerit Wagner <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Poetry updater <[email protected]> Co-authored-by: Carlo <[email protected]> Co-authored-by: olgagirona <[email protected]> Co-authored-by: julialopezmarti <[email protected]> Co-authored-by: trathienphuc-tran <[email protected]> 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update dependencies

6310e93

geritwagner merged commit 77c055e into main Sep 24, 2024
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geritwagner deleted the poetry_update branch September 24, 2024 04:16

julianprester pushed a commit that referenced this pull request Mar 7, 2025

update dependencies (#553)

29379ff

Co-authored-by: Poetry updater <[email protected]>

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