From bd386d6cf50b63a6dec05cb32f8cec1b87704f62 Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Mon, 26 Aug 2024 14:29:47 -0400
Subject: [PATCH 01/15] pin experiment

---
 .github/workflows/macos.yml | 4 ++--
 apis/python/conda-env.yml   | 4 ++--
 apis/python/pyproject.toml  | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
index 5367f0481..fbf28a6e3 100644
--- a/.github/workflows/macos.yml
+++ b/.github/workflows/macos.yml
@@ -87,7 +87,7 @@ jobs:
           environment-name: ci
           create-args: tiledb
       - name: Install dependencies
-        run: python -m pip install --prefer-binary pyarrow==10.0.1
+        run: python -m pip install --prefer-binary pyarrow==12
       - name: Build tiledbvcf-py
         env:
           LIBTILEDBVCF_PATH: "${{ github.workspace }}/dist"
@@ -164,7 +164,7 @@ jobs:
         with:
           python-version: "3.11"
       - name: Install dependencies
-        run: python -m pip install --prefer-binary pyarrow==10.0.1
+        run: python -m pip install --prefer-binary pyarrow==12
       - name: Build tiledbvcf-py
         run: cd apis/python && python -m pip install -v .[test]
       - name: Confirm linking
diff --git a/apis/python/conda-env.yml b/apis/python/conda-env.yml
index 9d632ab56..ad448421b 100644
--- a/apis/python/conda-env.yml
+++ b/apis/python/conda-env.yml
@@ -2,10 +2,10 @@ name: tiledbvcf-py
 channels:
   - conda-forge
 dependencies:
-  - numpy<2
+  - numpy
   - python<3.12 # based on available tiledb-py wheels
   - pybind11
-  - pyarrow>=14.0.2 # for pyarrow security fix
+  - pyarrow
   - fsspec
   - dask
   - pip
diff --git a/apis/python/pyproject.toml b/apis/python/pyproject.toml
index f984f995f..efece60f5 100644
--- a/apis/python/pyproject.toml
+++ b/apis/python/pyproject.toml
@@ -40,7 +40,7 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
 ]
 
-dependencies = ["pandas", "pyarrow", "pyarrow-hotfix", "numpy<2"]
+dependencies = ["pandas", "pyarrow", "pyarrow-hotfix", "numpy"]
 
 [project.optional-dependencies]
 test = ["dask[distributed]", "pytest", "tiledb"]

From 17c67fd0289aab12056083a5b772d78549c20389 Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Mon, 26 Aug 2024 16:50:07 -0400
Subject: [PATCH 02/15] remove macos pyarrow pin

---
 .github/workflows/macos.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
index fbf28a6e3..0a6dcf7c6 100644
--- a/.github/workflows/macos.yml
+++ b/.github/workflows/macos.yml
@@ -86,8 +86,8 @@ jobs:
         with:
           environment-name: ci
           create-args: tiledb
-      - name: Install dependencies
-        run: python -m pip install --prefer-binary pyarrow==12
+#      - name: Install dependencies
+#        run: python -m pip install --prefer-binary pyarrow==12
       - name: Build tiledbvcf-py
         env:
           LIBTILEDBVCF_PATH: "${{ github.workspace }}/dist"
@@ -163,8 +163,8 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"
-      - name: Install dependencies
-        run: python -m pip install --prefer-binary pyarrow==12
+#      - name: Install dependencies
+#        run: python -m pip install --prefer-binary pyarrow==12
       - name: Build tiledbvcf-py
         run: cd apis/python && python -m pip install -v .[test]
       - name: Confirm linking

From eb6bc5a77edcef6f5bf53bae2a1ff8aeebd238d2 Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Tue, 27 Aug 2024 13:37:47 -0400
Subject: [PATCH 03/15] enable debug messages

---
 apis/python/tests/test_tiledbvcf.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/apis/python/tests/test_tiledbvcf.py b/apis/python/tests/test_tiledbvcf.py
index 67a5ef6bd..05c0aaa4d 100755
--- a/apis/python/tests/test_tiledbvcf.py
+++ b/apis/python/tests/test_tiledbvcf.py
@@ -70,6 +70,7 @@ def test_ds_attrs():
 
 
 def test_basic_count(test_ds):
+    tiledbvcf.config_logging("trace")
     assert test_ds.count() == 14
 
 

From cce4c99a33bf3e29f4d6e627775f9c008fc71f42 Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Tue, 27 Aug 2024 13:48:25 -0400
Subject: [PATCH 04/15] verbose pytest

---
 .github/workflows/macos.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
index 0a6dcf7c6..6230001b0 100644
--- a/.github/workflows/macos.yml
+++ b/.github/workflows/macos.yml
@@ -178,4 +178,4 @@ jobs:
       - name: Install bcftools (for tests)
         run: brew install bcftools
       - name: Test tiledbvcf-py
-        run: cd apis/python && pytest
+        run: cd apis/python && pytest -svvv

From ad365ec679b1b134a3718f78994e290a482cd1f0 Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Tue, 27 Aug 2024 15:13:21 -0400
Subject: [PATCH 05/15] skip s3 test

---
 apis/python/tests/test_tiledbvcf.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/apis/python/tests/test_tiledbvcf.py b/apis/python/tests/test_tiledbvcf.py
index 05c0aaa4d..47ea484b8 100755
--- a/apis/python/tests/test_tiledbvcf.py
+++ b/apis/python/tests/test_tiledbvcf.py
@@ -438,6 +438,8 @@ def test_read_var_length_filters(tmp_path):
     ds.ingest_samples(samples)
 
     ds = tiledbvcf.Dataset(uri, mode="r")
+
+    tiledbvcf.config_logging("trace")
     df = ds.read(["pos_start", "filters"])
 
     expected_df = pd.DataFrame(
@@ -913,7 +915,7 @@ def test_sample_and_region_partitioned_read():
     assert len(df) == 0
 
 
-@pytest.mark.skipif(os.environ.get("CI") != "true", reason="CI only")
+@pytest.mark.skip
 def test_large_export_correctness():
     uri = "s3://tiledb-inc-demo-data/tiledbvcf-arrays/v4/vcf-samples-20"
 

From 655f4c8fec71da0a326c1fb0a40e46b3a5e8450c Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Tue, 27 Aug 2024 18:31:39 -0400
Subject: [PATCH 06/15] cleanup

---
 .github/workflows/macos.yml           | 6 +-----
 apis/python/pyproject.toml            | 6 +++---
 apis/python/src/tiledbvcf/__init__.py | 1 -
 apis/python/tests/test_tiledbvcf.py   | 2 ++
 4 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
index 6230001b0..96752bd51 100644
--- a/.github/workflows/macos.yml
+++ b/.github/workflows/macos.yml
@@ -86,8 +86,6 @@ jobs:
         with:
           environment-name: ci
           create-args: tiledb
-#      - name: Install dependencies
-#        run: python -m pip install --prefer-binary pyarrow==12
       - name: Build tiledbvcf-py
         env:
           LIBTILEDBVCF_PATH: "${{ github.workspace }}/dist"
@@ -163,8 +161,6 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"
-#      - name: Install dependencies
-#        run: python -m pip install --prefer-binary pyarrow==12
       - name: Build tiledbvcf-py
         run: cd apis/python && python -m pip install -v .[test]
       - name: Confirm linking
@@ -178,4 +174,4 @@ jobs:
       - name: Install bcftools (for tests)
         run: brew install bcftools
       - name: Test tiledbvcf-py
-        run: cd apis/python && pytest -svvv
+        run: cd apis/python && pytest
diff --git a/apis/python/pyproject.toml b/apis/python/pyproject.toml
index efece60f5..c055bbb5c 100644
--- a/apis/python/pyproject.toml
+++ b/apis/python/pyproject.toml
@@ -29,18 +29,18 @@ dynamic = ["version"]
 description = "TileDB-VCF Python client"
 license = { text = "MIT" }
 authors = []
-requires-python = "~=3.8"
+requires-python = "~=3.9"
 classifiers = [
     "Development Status :: 4 - Beta",
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 
-dependencies = ["pandas", "pyarrow", "pyarrow-hotfix", "numpy"]
+dependencies = ["pandas", "pyarrow", "numpy"]
 
 [project.optional-dependencies]
 test = ["dask[distributed]", "pytest", "tiledb"]
diff --git a/apis/python/src/tiledbvcf/__init__.py b/apis/python/src/tiledbvcf/__init__.py
index 2e833e154..6a629c8ac 100644
--- a/apis/python/src/tiledbvcf/__init__.py
+++ b/apis/python/src/tiledbvcf/__init__.py
@@ -1,6 +1,5 @@
 # Initialize pyarrow first.
 import pyarrow
-import pyarrow_hotfix
 
 import ctypes
 import os
diff --git a/apis/python/tests/test_tiledbvcf.py b/apis/python/tests/test_tiledbvcf.py
index 47ea484b8..156db27b1 100755
--- a/apis/python/tests/test_tiledbvcf.py
+++ b/apis/python/tests/test_tiledbvcf.py
@@ -915,6 +915,8 @@ def test_sample_and_region_partitioned_read():
     assert len(df) == 0
 
 
+# TODO: enable after fixing issue with AWSSDK and pyarrow
+# @pytest.mark.skipif(os.environ.get("CI") != "true", reason="CI only")
 @pytest.mark.skip
 def test_large_export_correctness():
     uri = "s3://tiledb-inc-demo-data/tiledbvcf-arrays/v4/vcf-samples-20"

From d24b23d87a9aad12124172945e01f075fe6f2bd0 Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Tue, 27 Aug 2024 18:53:54 -0400
Subject: [PATCH 07/15] remove unused files

---
 .azure-pipelines.yml                |  4 ----
 apis/python/conda-env.yml           | 17 -----------------
 apis/python/tests/test_tiledbvcf.py |  3 ---
 docker/Dockerfile-dask-py           | 25 -------------------------
 4 files changed, 49 deletions(-)
 delete mode 100644 apis/python/conda-env.yml
 delete mode 100644 docker/Dockerfile-dask-py

diff --git a/.azure-pipelines.yml b/.azure-pipelines.yml
index 820005f39..f84d8da51 100644
--- a/.azure-pipelines.yml
+++ b/.azure-pipelines.yml
@@ -53,10 +53,6 @@ stages:
               repository: tiledb/tiledbvcf-py
               context: .
               test_cmd: -c "import tiledbvcf; print(tiledbvcf.version)"
-            # dask:
-            #   dockerfile: docker/Dockerfile-dask-py
-            #   repository: tiledb/tiledbvcf-dask
-            #   context: .
         steps:
         - template: ci/build-images.yml
 
diff --git a/apis/python/conda-env.yml b/apis/python/conda-env.yml
deleted file mode 100644
index ad448421b..000000000
--- a/apis/python/conda-env.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-name: tiledbvcf-py
-channels:
-  - conda-forge
-dependencies:
-  - numpy
-  - python<3.12 # based on available tiledb-py wheels
-  - pybind11
-  - pyarrow
-  - fsspec
-  - dask
-  - pip
-  - setuptools
-  - setuptools_scm
-  - setuptools_scm_git_archive
-  - pip:
-    - pytest
-    - pytest-runner
diff --git a/apis/python/tests/test_tiledbvcf.py b/apis/python/tests/test_tiledbvcf.py
index 156db27b1..f8de35f63 100755
--- a/apis/python/tests/test_tiledbvcf.py
+++ b/apis/python/tests/test_tiledbvcf.py
@@ -70,7 +70,6 @@ def test_ds_attrs():
 
 
 def test_basic_count(test_ds):
-    tiledbvcf.config_logging("trace")
     assert test_ds.count() == 14
 
 
@@ -438,8 +437,6 @@ def test_read_var_length_filters(tmp_path):
     ds.ingest_samples(samples)
 
     ds = tiledbvcf.Dataset(uri, mode="r")
-
-    tiledbvcf.config_logging("trace")
     df = ds.read(["pos_start", "filters"])
 
     expected_df = pd.DataFrame(
diff --git a/docker/Dockerfile-dask-py b/docker/Dockerfile-dask-py
deleted file mode 100644
index 9f61f9fa0..000000000
--- a/docker/Dockerfile-dask-py
+++ /dev/null
@@ -1,25 +0,0 @@
-FROM daskdev/dask:latest
-
-RUN conda config --prepend channels conda-forge
-
-# Install some dependencies
-RUN apt-get update \
-    && apt-get install --no-install-recommends -y \
-    wget cmake git gcc g++ build-essential autoconf automake \
-    libssl-dev libbz2-dev liblz4-dev libcurl4-openssl-dev \
-    zlib1g-dev liblzma-dev \
-    python3 python3-dev python3-venv \
-    ninja-build \
-    && rm -rf /var/lib/apt/lists/*
-
-# Copy the TileDB-VCF Python directory and build it.
-WORKDIR /tmp/
-COPY . tiledbvcf
-RUN cd tiledbvcf \
-    && rm -rf libtiledbvcf/build dist \
-    && cd apis/python \
-    && conda env update -n base -f conda-env.yml \
-    && pip install -v . \
-    && cd /tmp \
-    && rm -rf tiledbvcf \
-    && conda clean -a -y

From b0ac46c9f14c6e4b4708f88a97cfc4a9c80d3c96 Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Tue, 27 Aug 2024 19:13:42 -0400
Subject: [PATCH 08/15] add windows utf-8 compiler flag

---
 libtiledbvcf/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/libtiledbvcf/CMakeLists.txt b/libtiledbvcf/CMakeLists.txt
index 691fe52b8..76a09aac6 100644
--- a/libtiledbvcf/CMakeLists.txt
+++ b/libtiledbvcf/CMakeLists.txt
@@ -96,6 +96,7 @@ if(WIN32 AND NOT MSYS)
   endif()
   # /wd4996 - no deprecated
   add_compile_options(/wd4996)
+  add_compile_options(/utf-8)
 else()
   if (BUILD_TYPE STREQUAL "DEBUG")
     add_compile_options(-DDEBUG -O0 -g3 -ggdb3 -gdwarf-3 -Wall)

From 009ff67cbfeb9a708f007db1213d8f14f7443a6a Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Tue, 27 Aug 2024 21:10:59 -0400
Subject: [PATCH 09/15] windows updates

---
 ci/gha-win-env.yml                 | 13 +++----------
 libtiledbvcf/src/vcf/vcf_merger.cc | 15 +++++++++++++++
 2 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/ci/gha-win-env.yml b/ci/gha-win-env.yml
index 8289dae4b..d81870409 100644
--- a/ci/gha-win-env.yml
+++ b/ci/gha-win-env.yml
@@ -8,22 +8,15 @@ dependencies:
   - cmake
   - git
   - m2w64-htslib
-  - tiledb=2.15
   - vs2019_win-64
   # build tiledbvcf-py
-  - numpy<2
-  - pandas<2.0
-  - pyarrow=9.0
-  - pyarrow-hotfix
+  - numpy
+  - pandas
+  - pyarrow
   - pybind11
   - python
   - rpdb
-  - setuptools
-  - setuptools_scm=6.0.1
-  - setuptools_scm_git_archive
-  - wheel
   # test tiledbvcf-py
   - dask
-  - fsspec<2023.3.0
   - pytest
   - tiledb-py
diff --git a/libtiledbvcf/src/vcf/vcf_merger.cc b/libtiledbvcf/src/vcf/vcf_merger.cc
index f60348048..acf0f67eb 100644
--- a/libtiledbvcf/src/vcf/vcf_merger.cc
+++ b/libtiledbvcf/src/vcf/vcf_merger.cc
@@ -595,8 +595,23 @@ void VCFMerger::finish_merge() {
   rec->pos = md_.pos;
 
   // ID
+#ifdef _WIN32
+  // Workaround for windows python feedstock build, since fmt::join is not
+  // available
+  std::string ids{"."};
+  if (!md_.ids.empty()) {
+    std::ostringstream oss;
+    std::copy(
+        md_.ids.begin(),
+        md_.ids.end() - 1,
+        std::ostream_iterator<std::string>(oss, ";"));
+    oss << md_.ids.back();
+    ids = oss.str();
+  }
+#else
   std::string ids =
       md_.ids.size() ? fmt::format("{}", fmt::join(md_.ids, ";")) : ".";
+#endif
   bcf_update_id(hdr_.get(), rec.get(), ids.c_str());
 
   // REF, ALT

From ea69a3f9f63c936de3a38235d4662d2aee8df983 Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Tue, 27 Aug 2024 21:24:42 -0400
Subject: [PATCH 10/15] fix windows build

---
 ci/gha-win-env.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ci/gha-win-env.yml b/ci/gha-win-env.yml
index d81870409..ccafcc7b3 100644
--- a/ci/gha-win-env.yml
+++ b/ci/gha-win-env.yml
@@ -8,6 +8,7 @@ dependencies:
   - cmake
   - git
   - m2w64-htslib
+  - tiledb
   - vs2019_win-64
   # build tiledbvcf-py
   - numpy

From 5301c5638868c241f26a79ceb3b6f9496d045fa5 Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Tue, 27 Aug 2024 21:41:24 -0400
Subject: [PATCH 11/15] windows build experiment

---
 ci/gha-win-env.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/ci/gha-win-env.yml b/ci/gha-win-env.yml
index ccafcc7b3..7d2f72363 100644
--- a/ci/gha-win-env.yml
+++ b/ci/gha-win-env.yml
@@ -8,7 +8,7 @@ dependencies:
   - cmake
   - git
   - m2w64-htslib
-  - tiledb
+  - tiledb=2.15
   - vs2019_win-64
   # build tiledbvcf-py
   - numpy
@@ -17,7 +17,12 @@ dependencies:
   - pybind11
   - python
   - rpdb
+  - setuptools
+  - setuptools_scm=6.0.1
+  - setuptools_scm_git_archive
+  - wheel
   # test tiledbvcf-py
   - dask
+  - fsspec<2023.3.0
   - pytest
   - tiledb-py

From cc31fbd47e6db147f4dd5cc829fb5a1fa1046180 Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Tue, 27 Aug 2024 21:58:08 -0400
Subject: [PATCH 12/15] revert windows env

---
 ci/gha-win-env.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/ci/gha-win-env.yml b/ci/gha-win-env.yml
index 7d2f72363..8289dae4b 100644
--- a/ci/gha-win-env.yml
+++ b/ci/gha-win-env.yml
@@ -11,9 +11,10 @@ dependencies:
   - tiledb=2.15
   - vs2019_win-64
   # build tiledbvcf-py
-  - numpy
-  - pandas
-  - pyarrow
+  - numpy<2
+  - pandas<2.0
+  - pyarrow=9.0
+  - pyarrow-hotfix
   - pybind11
   - python
   - rpdb

From fd511529dc48d79dd34c17d5d94c938637bd3153 Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Wed, 28 Aug 2024 08:54:59 -0400
Subject: [PATCH 13/15] update nightly

---
 ci/nightly/build-tiledb-py.sh    | 2 +-
 ci/nightly/build-tiledbvcf-py.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci/nightly/build-tiledb-py.sh b/ci/nightly/build-tiledb-py.sh
index bbc988ace..d9e297458 100644
--- a/ci/nightly/build-tiledb-py.sh
+++ b/ci/nightly/build-tiledb-py.sh
@@ -19,7 +19,7 @@ fi
 export TILEDB_PATH=$GITHUB_WORKSPACE/install/
 
 cd TileDB-Py/
-python -m pip install -Cskbuild.cmake.define.TILEDB_REMOVE_DEPRECATIONS=OFF -v . pyarrow==12
+python -m pip install -Cskbuild.cmake.define.TILEDB_REMOVE_DEPRECATIONS=OFF -v .
 
 # Can't run the import inside of the Git repo because Python automatically looks
 # for `./module/__init.py__`
diff --git a/ci/nightly/build-tiledbvcf-py.sh b/ci/nightly/build-tiledbvcf-py.sh
index ef50f77ce..54fc1af45 100644
--- a/ci/nightly/build-tiledbvcf-py.sh
+++ b/ci/nightly/build-tiledbvcf-py.sh
@@ -20,7 +20,7 @@ fi
 export LIBTILEDBVCF_PATH=$GITHUB_WORKSPACE/install/
 
 cd TileDB-VCF/apis/python
-python -m pip install .[test] pyarrow==12
+python -m pip install .[test]
 python -c "import tiledbvcf; print(tiledbvcf.version)"
 
 pytest

From 7471a5d7f36d6e2a846e1bf249451d552d662e7c Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Wed, 28 Aug 2024 18:07:01 -0400
Subject: [PATCH 14/15] review feedback

---
 apis/python/pyproject.toml          | 2 +-
 apis/python/tests/test_tiledbvcf.py | 2 +-
 ci/gha-win-env.yml                  | 9 ++++-----
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/apis/python/pyproject.toml b/apis/python/pyproject.toml
index c055bbb5c..bc179fd86 100644
--- a/apis/python/pyproject.toml
+++ b/apis/python/pyproject.toml
@@ -40,7 +40,7 @@ classifiers = [
     "Programming Language :: Python :: 3.12",
 ]
 
-dependencies = ["pandas", "pyarrow", "numpy"]
+dependencies = ["pandas", "pyarrow>=14.0.1", "numpy"]
 
 [project.optional-dependencies]
 test = ["dask[distributed]", "pytest", "tiledb"]
diff --git a/apis/python/tests/test_tiledbvcf.py b/apis/python/tests/test_tiledbvcf.py
index f8de35f63..af58cbc5a 100755
--- a/apis/python/tests/test_tiledbvcf.py
+++ b/apis/python/tests/test_tiledbvcf.py
@@ -912,7 +912,7 @@ def test_sample_and_region_partitioned_read():
     assert len(df) == 0
 
 
-# TODO: enable after fixing issue with AWSSDK and pyarrow
+# TODO: enable after libtiledb 2.26.0 is released (https://github.com/TileDB-Inc/TileDB/pull/5223)
 # @pytest.mark.skipif(os.environ.get("CI") != "true", reason="CI only")
 @pytest.mark.skip
 def test_large_export_correctness():
diff --git a/ci/gha-win-env.yml b/ci/gha-win-env.yml
index 8289dae4b..017ca5ae7 100644
--- a/ci/gha-win-env.yml
+++ b/ci/gha-win-env.yml
@@ -8,13 +8,12 @@ dependencies:
   - cmake
   - git
   - m2w64-htslib
-  - tiledb=2.15
+  - tiledb=2.25
   - vs2019_win-64
   # build tiledbvcf-py
-  - numpy<2
-  - pandas<2.0
-  - pyarrow=9.0
-  - pyarrow-hotfix
+  - numpy
+  - pandas
+  - pyarrow>=14.0.1
   - pybind11
   - python
   - rpdb

From 5c1ec43becfe00a12b5ed80c70d9048a2a036d6b Mon Sep 17 00:00:00 2001
From: George Powley <george.powley@gmail.com>
Date: Mon, 14 Oct 2024 12:38:01 -0400
Subject: [PATCH 15/15] merge main; enable test

---
 apis/python/tests/test_tiledbvcf.py |  4 +---
 libtiledbvcf/CMakeLists.txt         |  1 -
 libtiledbvcf/src/vcf/vcf_merger.cc  | 15 ---------------
 3 files changed, 1 insertion(+), 19 deletions(-)

diff --git a/apis/python/tests/test_tiledbvcf.py b/apis/python/tests/test_tiledbvcf.py
index 3eeab0090..95718f2a0 100755
--- a/apis/python/tests/test_tiledbvcf.py
+++ b/apis/python/tests/test_tiledbvcf.py
@@ -930,9 +930,7 @@ def test_sample_and_region_partitioned_read():
     assert len(df) == 0
 
 
-# TODO: enable after libtiledb 2.26.0 is released (https://github.com/TileDB-Inc/TileDB/pull/5223)
-# @pytest.mark.skipif(os.environ.get("CI") != "true", reason="CI only")
-@pytest.mark.skip
+@pytest.mark.skipif(os.environ.get("CI") != "true", reason="CI only")
 def test_large_export_correctness():
     uri = "s3://tiledb-inc-demo-data/tiledbvcf-arrays/v4/vcf-samples-20"
 
diff --git a/libtiledbvcf/CMakeLists.txt b/libtiledbvcf/CMakeLists.txt
index 76a09aac6..691fe52b8 100644
--- a/libtiledbvcf/CMakeLists.txt
+++ b/libtiledbvcf/CMakeLists.txt
@@ -96,7 +96,6 @@ if(WIN32 AND NOT MSYS)
   endif()
   # /wd4996 - no deprecated
   add_compile_options(/wd4996)
-  add_compile_options(/utf-8)
 else()
   if (BUILD_TYPE STREQUAL "DEBUG")
     add_compile_options(-DDEBUG -O0 -g3 -ggdb3 -gdwarf-3 -Wall)
diff --git a/libtiledbvcf/src/vcf/vcf_merger.cc b/libtiledbvcf/src/vcf/vcf_merger.cc
index acf0f67eb..f60348048 100644
--- a/libtiledbvcf/src/vcf/vcf_merger.cc
+++ b/libtiledbvcf/src/vcf/vcf_merger.cc
@@ -595,23 +595,8 @@ void VCFMerger::finish_merge() {
   rec->pos = md_.pos;
 
   // ID
-#ifdef _WIN32
-  // Workaround for windows python feedstock build, since fmt::join is not
-  // available
-  std::string ids{"."};
-  if (!md_.ids.empty()) {
-    std::ostringstream oss;
-    std::copy(
-        md_.ids.begin(),
-        md_.ids.end() - 1,
-        std::ostream_iterator<std::string>(oss, ";"));
-    oss << md_.ids.back();
-    ids = oss.str();
-  }
-#else
   std::string ids =
       md_.ids.size() ? fmt::format("{}", fmt::join(md_.ids, ";")) : ".";
-#endif
   bcf_update_id(hdr_.get(), rec.get(), ids.c_str());
 
   // REF, ALT