Merge branch 'release/v0.12.0'

usnistgov · Nov 4, 2024 · 3f379da · 3f379da
2 parents 4de6354 + ffcf5a4
commit 3f379da
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diff --git a/.cruft.json b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/usnistgov/cookiecutter-nist-python.git",
-  "commit": "8fe5103d25de7e7d13d400f599c6653866a69afc",
+  "commit": "714e872b2f122570895ef79d72f5a364f6f9b12b",
   "checkout": "develop",
   "context": {
     "cookiecutter": {

diff --git a/.git_archival.txt b/.git_archival.txt
@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+.git_archival.txt  export-subst
diff --git a/.gitignore b/.gitignore
@@ -100,8 +100,19 @@ ENV/
 # mkdocs documentation
 /site
 
+# NOTE: use `/.mypy_cache/`, etc because want to flag those in other
 # mypy
 .mypy_cache/
+.dmypy.json
+
+# pytpe
+.pytype/
+
+# ruff
+.ruff_cache
+
+# PDF output
+README.pdf
 
 # IDE settings
 .vscode/
@@ -117,6 +128,10 @@ cruft.patch
 /pyproject2conda-feedstock*/
 /src/**/_version.py
 tuna-loadtime.log
-/requirements/py*-dev.yaml
+/requirements/py*-dev-user.yaml
+/requirements/dev-user.txt
+/requirements/lock/py*-dev-user-conda-lock.yml*
+/requirements/lock/py*-dev-user.txt*
+
+# other
 /README.pdf
-/requirements/lock/py*-dev-conda-lock.yml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,4 +1,3 @@
----
 # pre-commit install
 # pre-commit run --all-files
 # See https://pre-commit.com for more information
@@ -9,137 +8,154 @@ default_install_hook_types:
 repos:
   # * Top level
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
       - id: check-added-large-files
-      - id: check-yaml
-      - id: check-json
+      - id: check-case-conflict
       - id: check-merge-conflict
       - id: check-symlinks
+      - id: check-yaml
+      - id: check-json
       - id: check-toml
-  # * sync dependencies
-  # Put this first, because messes up formatting
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+  # * Sync dependencies
   - repo: https://github.com/mxr/sync-pre-commit-deps
     rev: v0.0.1
     hooks:
       - id: sync-pre-commit-deps
 
+  # * Pyproject-fmt
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: 2.2.4
+    hooks:
+      - id: pyproject-fmt
+        args: [--indent=4, --keep-full-version]
+        files: ^pyproject.toml$
+
   # * Prettier
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.0.3"
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         alias: markdownlint
-        stages: [commit]
+        stages: [pre-commit]
         additional_dependencies:
           - prettier-plugin-toml
-        exclude: ^requirements/lock/.*[.]yml|^.copier-answers.ya?ml
 
   # * Markdown
   - repo: https://github.com/DavidAnson/markdownlint-cli2
-    rev: v0.10.0
+    rev: v0.14.0
     hooks:
       - id: markdownlint-cli2
-        args: ["--style prettier"]
+        alias: markdownlint
+        args: [--style, prettier]
 
   # * Linting
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    # Ruff version.
-    rev: "v0.1.3"
-    hooks:
-      - id: ruff
-  - repo: https://github.com/psf/black
-    rev: 23.10.1
-    hooks:
-      # NOTE: nbQA for notebook formatting
-      - id: black
+  # To be replace by ruff analog when I find one ...
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.16.0"
+    rev: 1.18.0
     hooks:
       - id: blacken-docs
         additional_dependencies:
-          - black==23.10.1
-        # exclude: ^README.md
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+          - black==24.4.2
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.6
+    hooks:
+      - id: ruff
+        alias: ruff-all
+        types_or: &ruff-types-or [python, pyi, jupyter]
+        args: [--fix, --show-fixes]
+      - id: ruff-format
+        alias: ruff-all
+        types_or: *ruff-types-or
+
+  # * Spelling
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
     hooks:
-      - id: nbqa-ruff
-        additional_dependencies: [ruff==0.1.3]
-      - id: nbqa-black
-        additional_dependencies: [black==23.10.1]
+      - id: codespell
+        additional_dependencies: [tomli]
+        args: [-I, docs/spelling_wordlist.txt]
+        exclude_types: [jupyter]
+
+  # * Notebook spelling
+  # - repo: https://github.com/nbQA-dev/nbQA
+  #   rev: 1.8.4
+  #   hooks:
+  #     - id: nbqa
+  #       alias: nbqa-codespell
+  #       name: nbqa-codespell
+  #       additional_dependencies: &codespell-deps [codespell==2.2.6, tomli] # make sure same as above
+  #       args:
+  #         [codespell, --ignore-words=docs/spelling_wordlist.txt, --nbqa-shell]
+  #     - id: nbqa
+  #       alias: nbqa-codespell
+  #       name: nbqa-codespell-markdown
+  #       additional_dependencies: *codespell-deps
+  #       args:
+  #         [
+  #           codespell,
+  #           --ignore-words=docs/spelling_wordlist.txt,
+  #           --nbqa-shell,
+  #           --nbqa-md,
+  #         ]
+
+  # * Strip out metadata from notebooks
+  # - repo: https://github.com/kynan/nbstripout
+  #   rev: 0.7.1
+  #   hooks:
+  #     - id: nbstripout
+  #       args: [
+  #           --keep-output, # keep output (needed for nbval testing)
+  #           --keep-count, # Errors with nbval without this...
+  #           --extra-keys, # strip out kernelspec.  If use this, always have to reselect kernel when open a notebook...
+  #           "metadata.kernelspec metadata.kernel_spec",
+  #         ]
 
   # * Commit message
   - repo: https://github.com/commitizen-tools/commitizen
-    rev: 3.12.0
+    rev: v3.29.0
     hooks:
       - id: commitizen
         stages: [commit-msg]
 
   # * Manual Linting ------------------------------------------------------------
-  # * isort, pyupgrade, flake8 defer to ruff
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        stages: [manual]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.17.0
     hooks:
       - id: pyupgrade
         stages: [manual]
         args: [--py38-plus]
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
-    hooks:
-      - id: flake8
-        stages: [manual]
-        additional_dependencies:
-          - flake8-docstrings
-          - Flake8-pyproject
-          # - pep8-naming
-          # - flake8-rst-docstrings
-        exclude: ^tests/|^src/pyproject2conda/tests/|^docs/conf.py|^setup.py
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
-    hooks:
-      - id: nbqa-pyupgrade
-        additional_dependencies: [pyupgrade]
-        stages: [manual]
-        args: [--py38-plus]
-      - id: nbqa-isort
-        additional_dependencies: [isort]
-        stages: [manual]
-  # ** spelling
-  - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+  # - repo: https://github.com/nbQA-dev/nbQA
+  #   rev: 1.8.4
+  #   hooks:
+  #     - id: nbqa-pyupgrade
+  #       additional_dependencies: [pyupgrade]
+  #       stages: [manual]
+  #       args: [--py38-plus]
+
+  # ** typos
+  # Probably stick with codespell, but this might also be nice...
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.24.6
     hooks:
-      - id: codespell
-        types_or: [python, rst, markdown, cython, c]
-        additional_dependencies: [tomli]
-        args: [-I, docs/spelling_wordlist.txt]
+      - id: typos
         stages: [manual]
-
-  # - repo: local
+        exclude: "[.]ipynb$"
+  # - repo: https://github.com/nbQA-dev/nbQA
+  #   rev: 1.8.4
   #   hooks:
-  #     - id: mypy
-  #       name: mypy
-  #       entry: tox
-  #       args: ["-e", "lint-mypy"]
-  #       language: system
-  #       pass_filenames: false
-  #       # additional_dependencies: [tox]
-  #       types: [python]
-  #       require_serial: true
+  #     - id: nbqa
+  #       alias: nbqa-typos
+  #       name: nbqa-typos
+  #       additional_dependencies: &typos-deps [typos==1.19.0] # make sure save version as above.
   #       stages: [manual]
-  #     - id: pyright
-  #       name: pyright
-  #       entry: pyright
-  #       args: []
-  #       language: system
-  #       pass_filenames: true
-  #       # additional_dependencies: [tox]
-  #       types: [python]
-  #       require_serial: true
+  #       args: [typos, --nbqa-shell]
+  #     - id: nbqa
+  #       alias: nbqa-typos
+  #       name: nbqa-typos-markdown
+  #       additional_dependencies: *typos-deps
   #       stages: [manual]
+  #       args: [typos, --nbqa-shell, --nbqa-md]
diff --git a/.prettierignore b/.prettierignore
@@ -0,0 +1,11 @@
+# Ignore file for prettier
+# Similar to .gitignore
+
+# Use pyproject-fmt for pyproject.toml
+pyproject.toml
+
+# Don't fix yaml files under requirements/lock.  These are created by conda-lock.
+/requirements/lock/*.y*ml
+
+# Don't fix copier answers
+.copier-answers.y*ml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,36 @@ See the fragment files in [changelog.d]
 
 <!-- scriv-insert-here -->
 
+## v0.12.0 — 2024-11-04
+
+### Removed
+
+- Removed comments based (`# p2c: ...`) support. Specify changes with
+  `tool.pyproject2conda.dependencies` table only. This greatly simplifies the
+  code, and has become the primary way to use the `pyproject2conda`.
+
+### Added
+
+- Added [PEP 735](https://peps.python.org/pep-0735/) support. This includes
+  adding option `--group` to the cli, and `groups` key to
+  `tools.pyproject2conda.envs....` tables. There is also an option
+  `--extra-or-group` (or `extras_or_groups` in pyproject.toml) that will first
+  try to find dependencies from "extras" and then from "groups".
+
+### Changed
+
+- Passing no extras to an environment now defaults to no added extras or groups.
+  Old behavior (to default to the extra with the same name as the environment)
+  was lead to complications with support of `dependency-groups`. Explicitly pass
+  the extra or group if to get the old behavior.
+- `default_envs` now passed the environment name as `extras_or_groups`.
+  Therefore, if the name of the environment is an extra, it will be used.
+  Otherwise, it will be from a group of that name.
+
+- Removed option `--base/--no-base`. Replaced with `--skip-package`. Default is
+  to include package dependencies. Pass `--skip-package` (or
+  `skip_package = true` in `pyproject.toml`) to skip package dependencies.
+
 ## v0.11.0 — 2023-11-28
 
 ### Added