From 8adcbcac049092f697bb39354366f73caa154b95 Mon Sep 17 00:00:00 2001 From: ErikDanielsson Date: Fri, 15 Aug 2025 13:58:15 +0200 Subject: [PATCH 1/6] Add fail to decode cases to enum. Improve output --- nf_core/components/components_differ.py | 161 ++++++++++++++++-------- 1 file changed, 109 insertions(+), 52 deletions(-) diff --git a/nf_core/components/components_differ.py b/nf_core/components/components_differ.py index 785389c721..4b38220cf7 100644 --- a/nf_core/components/components_differ.py +++ b/nf_core/components/components_differ.py @@ -3,6 +3,7 @@ import json import logging import os +from collections.abc import Iterator from pathlib import Path from typing import Union @@ -32,6 +33,8 @@ class DiffEnum(enum.Enum): CHANGED = enum.auto() CREATED = enum.auto() REMOVED = enum.auto() + FROM_DECODE_FAIL = enum.auto() + TO_DECODE_FAIL = enum.auto() @staticmethod def get_component_diffs(from_dir, to_dir, for_git=True, dsp_from_dir=None, dsp_to_dir=None): @@ -74,54 +77,88 @@ def get_component_diffs(from_dir, to_dir, for_git=True, dsp_from_dir=None, dsp_t # Loop through all the component files and compute their diffs if needed for file in files: - temp_path = Path(to_dir, file) - curr_path = Path(from_dir, file) - if temp_path.exists() and curr_path.exists() and temp_path.is_file(): + try: + diffs[file] = ComponentsDiffer.get_file_diff( + file=file, + to_dir=to_dir, + from_dir=from_dir, + dsp_to_dir=dsp_to_dir, + dsp_from_dir=dsp_from_dir, + ) + + except UnicodeDecodeError as e: + # We tried to decode a file we cannot decode, such as a vim .swp file + # Let's fail gracefully + diffs[file] = (ComponentsDiffer.FAILED, e) + + return diffs + + @staticmethod + def get_file_diff( + file, to_dir, from_dir, dsp_to_dir, dsp_from_dir + ) -> tuple[DiffEnum, Union[Iterator[str], UnicodeDecodeError]]: + temp_path = Path(to_dir, file) + curr_path = Path(from_dir, file) + if temp_path.exists() and curr_path.exists() and temp_path.is_file(): + try: with open(temp_path) as fh: new_lines = fh.readlines() + except UnicodeDecodeError as e: + return ComponentsDiffer.DiffEnum.TO_DECODE_FAIL, e + + try: with open(curr_path) as fh: old_lines = fh.readlines() + except UnicodeDecodeError as e: + return ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL, e - if new_lines == old_lines: - # The files are identical - diffs[file] = (ComponentsDiffer.DiffEnum.UNCHANGED, ()) - else: - # Compute the diff - diff = difflib.unified_diff( - old_lines, - new_lines, - fromfile=str(Path(dsp_from_dir, file)), - tofile=str(Path(dsp_to_dir, file)), - ) - diffs[file] = (ComponentsDiffer.DiffEnum.CHANGED, diff) - - elif temp_path.exists(): - with open(temp_path) as fh: - new_lines = fh.readlines() - # The file was created - # Show file against /dev/null + if new_lines == old_lines: + # The files are identical + return ComponentsDiffer.DiffEnum.UNCHANGED, iter(()) + else: + # Compute the diff diff = difflib.unified_diff( - [], + old_lines, new_lines, - fromfile=str(Path("/dev", "null")), + fromfile=str(Path(dsp_from_dir, file)), tofile=str(Path(dsp_to_dir, file)), ) - diffs[file] = (ComponentsDiffer.DiffEnum.CREATED, diff) + return ComponentsDiffer.DiffEnum.CHANGED, diff - elif curr_path.exists(): - # The file was removed - # Show file against /dev/null + elif temp_path.exists(): + try: + with open(temp_path) as fh: + new_lines = fh.readlines() + except UnicodeDecodeError as e: + return ComponentsDiffer.DiffEnum.TO_DECODE_FAIL, e + + # The file was created + # Show file against /dev/null + diff = difflib.unified_diff( + [], + new_lines, + fromfile=str(Path("/dev", "null")), + tofile=str(Path(dsp_to_dir, file)), + ) + return ComponentsDiffer.DiffEnum.CREATED, diff + elif curr_path.exists(): + # The file was removed + # Show file against /dev/null + try: with open(curr_path) as fh: old_lines = fh.readlines() - diff = difflib.unified_diff( - old_lines, - [], - fromfile=str(Path(dsp_from_dir, file)), - tofile=str(Path("/dev", "null")), - ) - diffs[file] = (ComponentsDiffer.DiffEnum.REMOVED, diff) - - return diffs + except UnicodeDecodeError as e: + return ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL, e + + diff = difflib.unified_diff( + old_lines, + [], + fromfile=str(Path(dsp_from_dir, file)), + tofile=str(Path("/dev", "null")), + ) + return ComponentsDiffer.DiffEnum.REMOVED, diff + else: + raise LookupError(f"The file {file} is missing both before and after the patch") @staticmethod def write_diff_file( @@ -188,6 +225,12 @@ def write_diff_file( elif diff_status == ComponentsDiffer.DiffEnum.REMOVED: # The file was removed between the commits fh.write(f"'{Path(dsp_from_dir, file)}' was removed\n") + elif diff_status == ComponentsDiffer.DiffEnum.TO_DECODE_FAIL: + # We failed to decode the file + log.warning(f"'{Path(dsp_to_dir, file)}' failed to be decoded\n") + elif diff_status == ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL: + # We failed to decode the file + log.warning(f"'{Path(dsp_from_dir, file)}' failed to be decoded\n") elif limit_output and not file.suffix == ".nf": # Skip printing the diff for files other than main.nf fh.write(f"Changes in '{Path(component, file)}' but not shown\n") @@ -280,32 +323,46 @@ def print_diff( for file, (diff_status, diff) in diffs.items(): if diff_status == ComponentsDiffer.DiffEnum.UNCHANGED: # The files are identical - log.info(f"'{Path(dsp_from_dir, file)}' is unchanged") + log.debug(f"'{Path(dsp_from_dir, file)}' is unchanged") + file_content = "Unchanged" elif diff_status == ComponentsDiffer.DiffEnum.CREATED: # The file was created between the commits - log.info(f"'{Path(dsp_from_dir, file)}' was created") + log.debug(f"'{Path(dsp_from_dir, file)}' was created") + file_content = "[green]Created[/]" elif diff_status == ComponentsDiffer.DiffEnum.REMOVED: # The file was removed between the commits - log.info(f"'{Path(dsp_from_dir, file)}' was removed") + log.debug(f"'{Path(dsp_from_dir, file)}' was removed") + file_content = "[red]Removed[/]" + elif diff_status == ComponentsDiffer.DiffEnum.TO_DECODE_FAIL: + # We failed to decode the file + log.debug(f"'{Path(dsp_to_dir, file)}' failed to be decoded") + file_content = ( + "[bold red]Failed to decode[/]. Please check if the file should be present in the directory" + ) + elif diff_status == ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL: + # We failed to decode the file + log.debug(f"'{Path(dsp_from_dir, file)}' failed to be decoded") + file_content = "[bold red]Failed to decode[/]. Please check the original file" elif limit_output and not file.suffix == ".nf": # Skip printing the diff for files other than main.nf - log.info(f"Changes in '{Path(component, file)}' but not shown") + log.debug(f"Changes in '{Path(component, file)}' but not shown") + file_content = Panel(f"Changes in '{Path(component, file)}' but not shown") else: # The file has changed - log.info(f"Changes in '{Path(component, file)}':") + log.debug(f"Changes in '{Path(component, file)}':") # Pretty print the diff using the pygments diff lexer - syntax = Syntax("".join(diff), "diff", theme="ansi_dark", line_numbers=True) - panel_group.append(Panel(syntax, title=str(file), title_align="left", padding=0)) - console.print( - Panel( - Group(*panel_group), - title=f"[white]{str(component)}[/white]", - title_align="left", - padding=0, - border_style="blue", - box=box.HEAVY, - ) + file_content = Syntax("".join(diff), "diff", theme="ansi_dark", line_numbers=True) + panel_group.append(Panel(file_content, title=str(file), title_align="left", padding=0)) + console.print( + Panel( + Group(*panel_group), + title=f"[white]{str(component)}[/white]", + title_align="left", + padding=0, + border_style="blue", + box=box.HEAVY, ) + ) @staticmethod def per_file_patch(patch_fn: Union[str, Path]) -> dict[str, list[str]]: From 9080a60dbb558e16b96f92e9e2a34f817cfb089f Mon Sep 17 00:00:00 2001 From: ErikDanielsson Date: Fri, 15 Aug 2025 14:32:45 +0200 Subject: [PATCH 2/6] Add questionary prompt to handle files that we failed to read --- nf_core/components/components_differ.py | 36 ++++++++++++++++++++----- nf_core/components/patch.py | 14 +++++++--- 2 files changed, 40 insertions(+), 10 deletions(-) diff --git a/nf_core/components/components_differ.py b/nf_core/components/components_differ.py index 4b38220cf7..658ea124ab 100644 --- a/nf_core/components/components_differ.py +++ b/nf_core/components/components_differ.py @@ -7,6 +7,7 @@ from pathlib import Path from typing import Union +import questionary from rich import box from rich.console import Console, Group, RenderableType from rich.panel import Panel @@ -227,10 +228,34 @@ def write_diff_file( fh.write(f"'{Path(dsp_from_dir, file)}' was removed\n") elif diff_status == ComponentsDiffer.DiffEnum.TO_DECODE_FAIL: # We failed to decode the file - log.warning(f"'{Path(dsp_to_dir, file)}' failed to be decoded\n") + log.warning( + f"We failed to read the [bold red]{file}[/] file. Please check that the component's directory contains only text files." + ) + ans = questionary.select( + "Do you still want to proceed with constructing the diff?", + choices=["Abort diff creation", "Ignore file", "Warn in diff"], + style=nf_core.utils.nfcore_question_style, + ).unsafe_ask() + if ans == "Warn in diff": + fh.write(f"'{Path(dsp_from_dir, file)}' failed to be decoded\n") + elif ans == "Abort diff creation": + raise OSError from diff + elif diff_status == ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL: # We failed to decode the file - log.warning(f"'{Path(dsp_from_dir, file)}' failed to be decoded\n") + log.warning( + f"We failed to read the [bold red]{file}[/] file. Please check that the component's directory contains only text files." + ) + ans = questionary.select( + "Do you still want to proceed with constructing the diff?", + choices=["Abort diff creation", "Ignore file", "Warn in diff"], + style=nf_core.utils.nfcore_question_style, + ).unsafe_ask() + if ans == "Warn in diff": + fh.write(f"'{Path(dsp_from_dir, file)}' failed to be decoded\n") + elif ans == "Abort diff creation": + raise OSError from diff + elif limit_output and not file.suffix == ".nf": # Skip printing the diff for files other than main.nf fh.write(f"Changes in '{Path(component, file)}' but not shown\n") @@ -336,13 +361,12 @@ def print_diff( elif diff_status == ComponentsDiffer.DiffEnum.TO_DECODE_FAIL: # We failed to decode the file log.debug(f"'{Path(dsp_to_dir, file)}' failed to be decoded") - file_content = ( - "[bold red]Failed to decode[/]. Please check if the file should be present in the directory" - ) + file_content = "[bold red]Failed to decode[/]" + file_content = "[bold red]Failed to decode new file[/]" elif diff_status == ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL: # We failed to decode the file log.debug(f"'{Path(dsp_from_dir, file)}' failed to be decoded") - file_content = "[bold red]Failed to decode[/]. Please check the original file" + file_content = "[bold red]Failed to decode old file[/]" elif limit_output and not file.suffix == ".nf": # Skip printing the diff for files other than main.nf log.debug(f"Changes in '{Path(component, file)}' but not shown") diff --git a/nf_core/components/patch.py b/nf_core/components/patch.py index 59ec7a381b..7c14f9f070 100644 --- a/nf_core/components/patch.py +++ b/nf_core/components/patch.py @@ -93,14 +93,13 @@ def patch(self, component=None): component_current_dir = Path(self.directory, component_relpath) patch_path = Path(self.directory, patch_relpath) + should_remove = False if patch_path.exists(): - remove = questionary.confirm( + should_remove = questionary.confirm( f"Patch exists for {self.component_type[:-1]} '{component_fullname}'. Do you want to regenerate it?", style=nf_core.utils.nfcore_question_style, ).unsafe_ask() - if remove: - os.remove(patch_path) - else: + if not should_remove: return # Create a temporary directory for storing the unchanged version of the module @@ -127,6 +126,9 @@ def patch(self, component=None): log.debug(f"Patch file wrote to a temporary directory {patch_temp_path}") except UserWarning: raise UserWarning(f"{self.component_type[:-1]} '{component_fullname}' is unchanged. No patch to compute") + except OSError: + log.info("Patch creation aborted by user") + return # Write changes to modules.json self.modules_json.add_patch_entry( @@ -144,6 +146,10 @@ def patch(self, component=None): dsp_to_dir=component_current_dir, ) + # Check if we should remove an old patch file + if should_remove: + os.remove(patch_path) + # Finally move the created patch file to its final location shutil.move(patch_temp_path, patch_path) log.info(f"Patch file of '{component_fullname}' written to '{patch_path}'") From 423daacb6c25625f41afc374f5cea3967c73652b Mon Sep 17 00:00:00 2001 From: ErikDanielsson Date: Fri, 15 Aug 2025 14:51:05 +0200 Subject: [PATCH 3/6] Move prompt to diff creator --- nf_core/components/components_differ.py | 89 ++++++++++++------------- 1 file changed, 44 insertions(+), 45 deletions(-) diff --git a/nf_core/components/components_differ.py b/nf_core/components/components_differ.py index 658ea124ab..022ea79b3e 100644 --- a/nf_core/components/components_differ.py +++ b/nf_core/components/components_differ.py @@ -5,7 +5,7 @@ import os from collections.abc import Iterator from pathlib import Path -from typing import Union +from typing import Optional, Union import questionary from rich import box @@ -75,29 +75,42 @@ def get_component_diffs(from_dir, to_dir, for_git=True, dsp_from_dir=None, dsp_t ) ) files = list(files) + log.info(files) # Loop through all the component files and compute their diffs if needed for file in files: - try: - diffs[file] = ComponentsDiffer.get_file_diff( - file=file, - to_dir=to_dir, - from_dir=from_dir, - dsp_to_dir=dsp_to_dir, - dsp_from_dir=dsp_from_dir, - ) - - except UnicodeDecodeError as e: - # We tried to decode a file we cannot decode, such as a vim .swp file - # Let's fail gracefully - diffs[file] = (ComponentsDiffer.FAILED, e) + log.info(file) + diff = ComponentsDiffer.get_file_diff( + file=file, + to_dir=to_dir, + from_dir=from_dir, + dsp_to_dir=dsp_to_dir, + dsp_from_dir=dsp_from_dir, + ) + if diff is not None: + diffs[file] = diff return diffs @staticmethod - def get_file_diff( - file, to_dir, from_dir, dsp_to_dir, dsp_from_dir - ) -> tuple[DiffEnum, Union[Iterator[str], UnicodeDecodeError]]: + def handle_decode_error(file, base_dir, type: DiffEnum, e: UnicodeDecodeError): + log.warning( + f"We failed to read the [bold red]{file}[/] file. Please check that the component's directory contains only text files." + ) + ans = questionary.select( + "Do you still want to proceed with constructing the diff?", + choices=["Abort diff creation", "Ignore file", "Warn in diff"], + style=nf_core.utils.nfcore_question_style, + ).unsafe_ask() + if ans == "Warn in diff": + return type, iter(()) + elif ans == "Abort diff creation": + raise OSError from e + else: + return None + + @staticmethod + def get_file_diff(file, to_dir, from_dir, dsp_to_dir, dsp_from_dir) -> Optional[tuple[DiffEnum, Iterator[str]]]: temp_path = Path(to_dir, file) curr_path = Path(from_dir, file) if temp_path.exists() and curr_path.exists() and temp_path.is_file(): @@ -105,13 +118,17 @@ def get_file_diff( with open(temp_path) as fh: new_lines = fh.readlines() except UnicodeDecodeError as e: - return ComponentsDiffer.DiffEnum.TO_DECODE_FAIL, e + return ComponentsDiffer.handle_decode_error( + file, dsp_to_dir, ComponentsDiffer.DiffEnum.TO_DECODE_FAIL, e + ) try: with open(curr_path) as fh: old_lines = fh.readlines() except UnicodeDecodeError as e: - return ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL, e + return ComponentsDiffer.handle_decode_error( + file, dsp_from_dir, ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL, e + ) if new_lines == old_lines: # The files are identical @@ -131,7 +148,9 @@ def get_file_diff( with open(temp_path) as fh: new_lines = fh.readlines() except UnicodeDecodeError as e: - return ComponentsDiffer.DiffEnum.TO_DECODE_FAIL, e + return ComponentsDiffer.handle_decode_error( + file, dsp_to_dir, ComponentsDiffer.DiffEnum.TO_DECODE_FAIL, e + ) # The file was created # Show file against /dev/null @@ -149,7 +168,9 @@ def get_file_diff( with open(curr_path) as fh: old_lines = fh.readlines() except UnicodeDecodeError as e: - return ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL, e + return ComponentsDiffer.handle_decode_error( + file, dsp_from_dir, ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL, e + ) diff = difflib.unified_diff( old_lines, @@ -228,33 +249,11 @@ def write_diff_file( fh.write(f"'{Path(dsp_from_dir, file)}' was removed\n") elif diff_status == ComponentsDiffer.DiffEnum.TO_DECODE_FAIL: # We failed to decode the file - log.warning( - f"We failed to read the [bold red]{file}[/] file. Please check that the component's directory contains only text files." - ) - ans = questionary.select( - "Do you still want to proceed with constructing the diff?", - choices=["Abort diff creation", "Ignore file", "Warn in diff"], - style=nf_core.utils.nfcore_question_style, - ).unsafe_ask() - if ans == "Warn in diff": - fh.write(f"'{Path(dsp_from_dir, file)}' failed to be decoded\n") - elif ans == "Abort diff creation": - raise OSError from diff + fh.write(f"'{Path(dsp_from_dir, file)}' failed to be decoded\n") elif diff_status == ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL: # We failed to decode the file - log.warning( - f"We failed to read the [bold red]{file}[/] file. Please check that the component's directory contains only text files." - ) - ans = questionary.select( - "Do you still want to proceed with constructing the diff?", - choices=["Abort diff creation", "Ignore file", "Warn in diff"], - style=nf_core.utils.nfcore_question_style, - ).unsafe_ask() - if ans == "Warn in diff": - fh.write(f"'{Path(dsp_from_dir, file)}' failed to be decoded\n") - elif ans == "Abort diff creation": - raise OSError from diff + fh.write(f"'{Path(dsp_from_dir, file)}' failed to be decoded\n") elif limit_output and not file.suffix == ".nf": # Skip printing the diff for files other than main.nf From e76e32e6bdedbf3edd05d3bb4fa8ff33e48255d9 Mon Sep 17 00:00:00 2001 From: ErikDanielsson Date: Fri, 15 Aug 2025 16:30:09 +0200 Subject: [PATCH 4/6] Add ignore list --- nf_core/components/components_differ.py | 60 ++++++++++++++++--------- nf_core/components/patch.py | 3 ++ 2 files changed, 43 insertions(+), 20 deletions(-) diff --git a/nf_core/components/components_differ.py b/nf_core/components/components_differ.py index 022ea79b3e..66a41ae735 100644 --- a/nf_core/components/components_differ.py +++ b/nf_core/components/components_differ.py @@ -38,7 +38,7 @@ class DiffEnum(enum.Enum): TO_DECODE_FAIL = enum.auto() @staticmethod - def get_component_diffs(from_dir, to_dir, for_git=True, dsp_from_dir=None, dsp_to_dir=None): + def get_component_diffs(from_dir, to_dir, for_git=True, dsp_from_dir=None, dsp_to_dir=None, ignore_files={}): """ Compute the diff between the current component version and the new version. @@ -86,6 +86,7 @@ def get_component_diffs(from_dir, to_dir, for_git=True, dsp_from_dir=None, dsp_t from_dir=from_dir, dsp_to_dir=dsp_to_dir, dsp_from_dir=dsp_from_dir, + ignore_files=ignore_files, ) if diff is not None: diffs[file] = diff @@ -93,24 +94,39 @@ def get_component_diffs(from_dir, to_dir, for_git=True, dsp_from_dir=None, dsp_t return diffs @staticmethod - def handle_decode_error(file, base_dir, type: DiffEnum, e: UnicodeDecodeError): - log.warning( - f"We failed to read the [bold red]{file}[/] file. Please check that the component's directory contains only text files." - ) - ans = questionary.select( - "Do you still want to proceed with constructing the diff?", - choices=["Abort diff creation", "Ignore file", "Warn in diff"], - style=nf_core.utils.nfcore_question_style, - ).unsafe_ask() - if ans == "Warn in diff": + def handle_decode_error(file, base_dir, type: DiffEnum, e: UnicodeDecodeError, ignore_files: dict[Path, bool]): + if file in ignore_files: + # We have already seen this file, so do not prompt again + ans = "i" if ignore_files[file] else "w" + else: + log.warning( + f"We failed to read the [bold red]{file}[/] file. Please check that the component's directory contains only text files." + ) + ans = questionary.select( + "Do you still want to proceed with constructing the diff?", + choices=[ + questionary.Choice("Abort diff creation", "a"), + questionary.Choice("Ignore file", "i"), + questionary.Choice("Warn in diff", "w"), + ], + style=nf_core.utils.nfcore_question_style, + ).unsafe_ask() + + if ans == "w": + ignore_files[file] = False return type, iter(()) - elif ans == "Abort diff creation": + elif ans == "a": raise OSError from e - else: + elif ans == "i": + ignore_files[file] = True return None + else: + raise UserWarning("This should never occur") @staticmethod - def get_file_diff(file, to_dir, from_dir, dsp_to_dir, dsp_from_dir) -> Optional[tuple[DiffEnum, Iterator[str]]]: + def get_file_diff( + file, to_dir, from_dir, dsp_to_dir, dsp_from_dir, ignore_files=[] + ) -> Optional[tuple[DiffEnum, Iterator[str]]]: temp_path = Path(to_dir, file) curr_path = Path(from_dir, file) if temp_path.exists() and curr_path.exists() and temp_path.is_file(): @@ -119,7 +135,7 @@ def get_file_diff(file, to_dir, from_dir, dsp_to_dir, dsp_from_dir) -> Optional[ new_lines = fh.readlines() except UnicodeDecodeError as e: return ComponentsDiffer.handle_decode_error( - file, dsp_to_dir, ComponentsDiffer.DiffEnum.TO_DECODE_FAIL, e + file, dsp_to_dir, ComponentsDiffer.DiffEnum.TO_DECODE_FAIL, e, ignore_files ) try: @@ -127,7 +143,7 @@ def get_file_diff(file, to_dir, from_dir, dsp_to_dir, dsp_from_dir) -> Optional[ old_lines = fh.readlines() except UnicodeDecodeError as e: return ComponentsDiffer.handle_decode_error( - file, dsp_from_dir, ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL, e + file, dsp_from_dir, ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL, e, ignore_files ) if new_lines == old_lines: @@ -149,7 +165,7 @@ def get_file_diff(file, to_dir, from_dir, dsp_to_dir, dsp_from_dir) -> Optional[ new_lines = fh.readlines() except UnicodeDecodeError as e: return ComponentsDiffer.handle_decode_error( - file, dsp_to_dir, ComponentsDiffer.DiffEnum.TO_DECODE_FAIL, e + file, dsp_to_dir, ComponentsDiffer.DiffEnum.TO_DECODE_FAIL, e, ignore_files ) # The file was created @@ -169,7 +185,7 @@ def get_file_diff(file, to_dir, from_dir, dsp_to_dir, dsp_from_dir) -> Optional[ old_lines = fh.readlines() except UnicodeDecodeError as e: return ComponentsDiffer.handle_decode_error( - file, dsp_from_dir, ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL, e + file, dsp_from_dir, ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL, e, ignore_files ) diff = difflib.unified_diff( @@ -196,6 +212,7 @@ def write_diff_file( dsp_from_dir=None, dsp_to_dir=None, limit_output=False, + ignore_files={}, ): """ Writes the diffs of a component to the diff file. @@ -223,7 +240,9 @@ def write_diff_file( if dsp_to_dir is None: dsp_to_dir = to_dir - diffs = ComponentsDiffer.get_component_diffs(from_dir, to_dir, for_git, dsp_from_dir, dsp_to_dir) + diffs = ComponentsDiffer.get_component_diffs( + from_dir, to_dir, for_git, dsp_from_dir, dsp_to_dir, ignore_files=ignore_files + ) if all(diff_status == ComponentsDiffer.DiffEnum.UNCHANGED for _, (diff_status, _) in diffs.items()): raise UserWarning("Component is unchanged") log.debug(f"Writing diff of '{component}' to '{diff_path}'") @@ -312,6 +331,7 @@ def print_diff( dsp_from_dir=None, dsp_to_dir=None, limit_output=False, + ignore_files={}, ): """ Prints the diffs between two component versions to the terminal @@ -333,7 +353,7 @@ def print_diff( dsp_to_dir = to_dir diffs = ComponentsDiffer.get_component_diffs( - from_dir, to_dir, for_git=False, dsp_from_dir=dsp_from_dir, dsp_to_dir=dsp_to_dir + from_dir, to_dir, for_git=False, dsp_from_dir=dsp_from_dir, dsp_to_dir=dsp_to_dir, ignore_files=ignore_files ) console = Console(force_terminal=nf_core.utils.rich_force_colors()) if current_version is not None and new_version is not None: diff --git a/nf_core/components/patch.py b/nf_core/components/patch.py index 7c14f9f070..948735f166 100644 --- a/nf_core/components/patch.py +++ b/nf_core/components/patch.py @@ -112,6 +112,7 @@ def patch(self, component=None): # Write the patch to a temporary location (otherwise it is printed to the screen later) patch_temp_path = tempfile.mktemp() + ignore_files = {} # This dict carries files which we have failed to read, and what we should do with them. Very hacky try: ComponentsDiffer.write_diff_file( patch_temp_path, @@ -122,6 +123,7 @@ def patch(self, component=None): for_git=False, dsp_from_dir=component_relpath, dsp_to_dir=component_relpath, + ignore_files=ignore_files, ) log.debug(f"Patch file wrote to a temporary directory {patch_temp_path}") except UserWarning: @@ -144,6 +146,7 @@ def patch(self, component=None): component_current_dir, dsp_from_dir=component_current_dir, dsp_to_dir=component_current_dir, + ignore_files=ignore_files, ) # Check if we should remove an old patch file From 0067542942a8e17f037100ef7a494cf6f7b7dce3 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 15 Aug 2025 14:38:18 +0000 Subject: [PATCH 5/6] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 184878d0fd..0aa7962018 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,7 @@ - Update pre-commit hook pre-commit/mirrors-mypy to v1.17.1 ([#3698](https://github.com/nf-core/tools/pull/3698)) - Update python:3.13-slim Docker digest to 4c2cf99 ([#3700](https://github.com/nf-core/tools/pull/3700)) - Validation of meta.yaml in cross-org repos ([#3680](https://github.com/nf-core/tools/pull/3680)) +- Patch patch command ([#3714](https://github.com/nf-core/tools/pull/3714)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] From 548cf05e3713171dda58f82cb6032b3773b65032 Mon Sep 17 00:00:00 2001 From: Erik Danielsson <53212377+ErikDanielsson@users.noreply.github.com> Date: Mon, 18 Aug 2025 22:22:02 +0200 Subject: [PATCH 6/6] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- nf_core/components/components_differ.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/nf_core/components/components_differ.py b/nf_core/components/components_differ.py index 66a41ae735..4756eadd32 100644 --- a/nf_core/components/components_differ.py +++ b/nf_core/components/components_differ.py @@ -79,7 +79,6 @@ def get_component_diffs(from_dir, to_dir, for_git=True, dsp_from_dir=None, dsp_t # Loop through all the component files and compute their diffs if needed for file in files: - log.info(file) diff = ComponentsDiffer.get_file_diff( file=file, to_dir=to_dir, @@ -100,7 +99,7 @@ def handle_decode_error(file, base_dir, type: DiffEnum, e: UnicodeDecodeError, i ans = "i" if ignore_files[file] else "w" else: log.warning( - f"We failed to read the [bold red]{file}[/] file. Please check that the component's directory contains only text files." + f"We failed to read the file: [bold red]{file}[/]. Please check that the component's directory contains only text files." ) ans = questionary.select( "Do you still want to proceed with constructing the diff?", @@ -380,7 +379,6 @@ def print_diff( elif diff_status == ComponentsDiffer.DiffEnum.TO_DECODE_FAIL: # We failed to decode the file log.debug(f"'{Path(dsp_to_dir, file)}' failed to be decoded") - file_content = "[bold red]Failed to decode[/]" file_content = "[bold red]Failed to decode new file[/]" elif diff_status == ComponentsDiffer.DiffEnum.FROM_DECODE_FAIL: # We failed to decode the file