Merge branch 'dev' into fork/DorielaGrabocka/collate_loci_action

Author: misialq

.copier-answers.yml

@@ -0,0 +1,12 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: dfb0404
+_src_path: https://github.com/qiime2/q2-setup-template.git
+module_name: types
+plugin_name: q2_types
+plugin_scripts: null
+project_author_email: [email protected]
+project_author_name: Greg Caporaso
+project_description: Common QIIME 2 semantic types.
+project_name: q2-types
+project_urls_homepage: https://qiime2.org
+project_urls_repository: https://github.com/qiime2/q2-types

.gitattributes

@@ -1 +1 @@
-q2_types/_version.py export-subst
+pyproject.toml export-subst

.github/workflows/ci-dev.yaml

@@ -10,3 +10,4 @@ jobs:
     uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml@dev
     with:
       distro: amplicon
+      recipe-path: 'conda-recipe'

.github/workflows/update-copyright-headers.yaml

@@ -0,0 +1,58 @@
+name: Update Copyright Headers
+
+on:
+  # Runs at 00:00 UTC on Jan 4th or via manual trigger
+  schedule:
+    - cron: '0 0 4 1 *'
+  workflow_dispatch:
+    inputs:
+      newYear:
+        description: "Desired year to update to (e.g., 2025). If not provided, will auto-detect."
+        required: false
+
+jobs:
+  update-headers:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Determine years for update
+        id: determine-years
+        run: |
+          INPUT_YEAR="${{ github.event.inputs.newYear }}"
+
+          if [ -z "$INPUT_YEAR" ]; then
+            CURRENT_YEAR="$(date +'%Y')"
+            echo "No 'newYear' input. Using current year: ${CURRENT_YEAR}"
+          else
+            CURRENT_YEAR="$INPUT_YEAR"
+            echo "Received user input. Updating to: ${CURRENT_YEAR}"
+          fi
+
+          echo "CURRENT_YEAR=$CURRENT_YEAR" >> $GITHUB_ENV
+
+      - name: Bump ending year in QIIME 2 headers
+        run: |
+          source $GITHUB_ENV
+
+          echo "Will update any QIIME 2 header years in [2015..$((CURRENT_YEAR-1))] to $CURRENT_YEAR"
+
+          for OLD_YEAR in $(seq 2015 $((CURRENT_YEAR - 1))); do
+            find . -type f -exec \
+              sed -i -E "s/(Copyright \(c\) [0-9]{4})-${OLD_YEAR}, QIIME 2/\1-${CURRENT_YEAR}, QIIME 2/g" {} +
+          done
+
+      - name: Commit and push changes
+        run: |
+          git config --global user.name "q2d2"
+          git config --global user.email "[email protected]"
+
+          if [ -n "$(git status --porcelain)" ]; then
+            git add .
+            git commit -m "Auto-update copyright year to $CURRENT_YEAR"
+            git push
+          else
+            echo "No changes to commit."
+            exit 0
+          fi

.gitignore

@@ -66,3 +66,7 @@ target/
 
 .DS_Store
 .vscode
+
+# Version file from versioningit
+_version.py
+

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2016-2023, QIIME 2 development team.
+Copyright (c) 2016-2025, QIIME 2 development team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

MANIFEST.in

@@ -15,7 +15,7 @@ test-cov: all
 	py.test --cov=q2_types
 
 install: all
-	$(PYTHON) setup.py install
+	$(PYTHON) -m pip install -v .
 
 dev: all
 	pip install -e .

Makefile

@@ -0,0 +1,43 @@
+package:
+  name: q2-types
+  version: {{ PLUGIN_VERSION }}
+source:
+  path: ..
+build:
+  script: make install
+requirements:
+  host:
+  - python {{ python }}
+  - setuptools
+  - versioningit
+  - wheel
+  run:
+  - python {{ python }}
+  - scikit-bio {{ scikit_bio }}
+  - scipy {{ scipy }}
+  - numpy
+  - pandas {{ pandas }}
+  - biom-format {{ biom_format }}
+  - ijson
+  - h5py
+  - qiime2 {{ qiime2_epoch }}.*
+  - samtools
+  - pyhmmer
+  - frictionless<=5.5.0
+  build:
+  - python {{ python }}
+  - setuptools
+  - versioningit
+test:
+  commands:
+  - py.test --pyargs q2_types
+  requires:
+  - pytest
+  - qiime2 >={{ qiime2 }}
+  imports:
+  - q2_types
+  - qiime2.plugins.types
+about:
+  home: https://qiime2.org
+  license: BSD-3-Clause
+  license_family: BSD

ci/recipe/meta.yaml

@@ -0,0 +1,50 @@
+[project]
+name = "q2-types"
+authors = [
+    { name = "Greg Caporaso", email = "[email protected]" }
+]
+description = "Common QIIME 2 semantic types."
+readme = {file = "README.md", content-type = "text/markdown"}
+license = {file = "LICENSE"}
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://qiime2.org"
+Repository = "https://github.com/qiime2/q2-types"
+
+[project.entry-points.'qiime2.plugins']
+"q2-types" = "q2_types.plugin_setup:plugin"
+
+[build-system]
+requires = [
+    "setuptools",
+    "versioningit",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"
+
+[tool.versioningit.vcs]
+method = "git-archive"
+describe-subst = "$Format:%(describe)$"
+default-tag = "0.0.1"
+
+[tool.versioningit.next-version]
+method = "minor"
+
+[tool.versioningit.format]
+distance = "{base_version}+{distance}.{vcs}{rev}"
+dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+
+[tool.versioningit.write]
+file = "q2_types/_version.py"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["q2_types*"]
+
+[tool.setuptools.package-data]
+q2_types = ["**/*"]

conda-recipe/meta.yaml

@@ -1,12 +1,13 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2023, QIIME 2 development team.
+# Copyright (c) 2016-2025, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-from ._version import get_versions
 
-__version__ = get_versions()['version']
-del get_versions
+try:
+    from ._version import __version__
+except ModuleNotFoundError:
+    __version__ = '0.0.0+notfound'

pyproject.toml

@@ -1,13 +1,15 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2023, QIIME 2 development team.
+# Copyright (c) 2016-2025, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 import gzip
 import itertools
+import re
 import warnings
+from collections import defaultdict
 from typing import List
 
 import skbio
@@ -138,3 +140,96 @@ def _validate_mag_ids(
                 "correctly. Printing duplicate MAG IDs: "
                 f"{set(duplicates)}"
             )
+
+
+class FileDictMixin:
+    def file_dict(self, relative=False):
+        """
+        For per sample directories it returns a mapping of sample id to
+        another dictionary where keys represent the file name and values
+        correspond to the filepath for each file matching the pathspec.
+        For files, it returns a mapping of file name to filepath for each
+        file matching the pathspec. If the dir format has the attribute
+        'suffixes', then these are removed from filenames.
+
+        Parameters
+        ---------
+        relative : bool
+            Whether to return filepaths relative to the directory's location.
+            Returns absolute filepaths by default.
+
+        Returns
+        -------
+        dict
+            Mapping of sample id -> filepath as described above.
+            Or mapping of sample id -> dict {filename: filepath} as
+            described above.
+            Both levels of the dictionary are sorted alphabetically by key.
+        """
+        file_pattern = re.compile(self.pathspec)
+        ids = defaultdict(dict)
+
+        for entry in self.path.iterdir():
+            if entry.is_dir():
+                outer_id = entry.name
+                for path in entry.iterdir():
+                    if file_pattern.match(path.name):
+
+                        file_path, inner_id = self._process_path(
+                            path=path,
+                            relative=relative,
+                        )
+
+                        ids[outer_id][inner_id] = file_path
+                ids[outer_id] = dict(sorted(ids[outer_id].items()))
+            else:
+                if file_pattern.match(entry.name):
+
+                    file_path, inner_id = self._process_path(
+                        path=entry,
+                        relative=relative,
+                    )
+
+                    ids[inner_id] = file_path
+
+        return dict(sorted(ids.items()))
+
+    def _process_path(self, path, relative=False):
+        """
+        This function processes the input file path to generate an absolute or
+        relative path string and the ID derived from the file name. The ID is
+        extracted by removing one of the suffixes from the file name. If the
+        class does not have a suffixes attribute, then the ID is defined to
+        be the filename.
+
+        Parameters:
+        ---------
+            path : Path
+                A Path object representing the file path to process.
+            relative : bool
+                A flag indicating whether the returned path should be relative
+                to the directory formats path or absolute.
+
+        Returns:
+        -------
+            processed_path : str
+                The relative or absolute path to the file.
+            _id : str
+                The ID derived from the file name.
+        """
+        file_name = path.stem
+        _id = file_name
+        suffixes = getattr(self, "suffixes", [])
+
+        if suffixes:
+            for suffix in suffixes:
+                if file_name.endswith(suffix):
+                    _id = file_name[:-len(suffix)]
+                    break
+
+        processed_path = (
+            path.absolute().relative_to(self.path.absolute())
+            if relative
+            else path.absolute()
+        )
+        return str(processed_path), _id