Merge branch 'release/v0.9.0'

.cruft.json

@@ -1,30 +1,23 @@
 {
   "template": "https://github.com/usnistgov/cookiecutter-nist-python.git",
-  "commit": "7ba78569cba4c2b39c2706d1f95b74c919b310cf",
+  "commit": "8fe5103d25de7e7d13d400f599c6653866a69afc",
   "checkout": "develop",
   "context": {
     "cookiecutter": {
+      "project_name": "pyproject2conda",
+      "project_slug": "pyproject2conda",
+      "project_short_description": "A script to convert a Python project declared on a pyproject.toml to a conda environment.",
       "full_name": "William P. Krekelberg",
       "email": "[email protected]",
       "github_username": "usnistgov",
       "pypi_username": "conda-forge",
       "conda_channel": "wpk-nist",
-      "project_name": "pyproject2conda",
-      "project_slug": "pyproject2conda",
-      "_copy_without_render": [
-        "*.html",
-        "docs/_templates/*.rst",
-        "docs/_templates/autosummary/*.rst",
-        "docs/_templates/autodocsumm/*.rst",
-        "docs/_static/css/*",
-        "docs/_static/js/*",
-        "changelog.d/templates/*.j2",
-        "changelog.d/templates/auto-changelog/*.jinja2"
-      ],
-      "project_short_description": "A script to convert a Python project declared on a pyproject.toml to a conda environment.",
-      "command_line_interface": "Typer",
-      "sphinx_use_autodocsumm": "y",
+      "command_line_interface": "typer",
+      "sphinx_use_autodocsumm": true,
       "sphinx_theme": "sphinx_book_theme",
+      "year": "2023",
+      "__answers": "",
+      "_copy_without_render": [],
       "_template": "https://github.com/usnistgov/cookiecutter-nist-python.git"
     }
   },

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ default_install_hook_types:
 repos:
   # * Top level
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -35,23 +35,23 @@ repos:
         stages: [commit]
         additional_dependencies:
           - prettier-plugin-toml
-        exclude: ^requirements/lock/.*[.]yml
+        exclude: ^requirements/lock/.*[.]yml|^.copier-answers.ya?ml
 
   # * Markdown
   - repo: https://github.com/DavidAnson/markdownlint-cli2
-    rev: v0.9.2
+    rev: v0.10.0
     hooks:
       - id: markdownlint-cli2
         args: ["--style prettier"]
 
   # * Linting
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     # Ruff version.
-    rev: "v0.0.289"
+    rev: "v0.1.3"
     hooks:
       - id: ruff
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 23.10.1
     hooks:
       # NOTE: nbQA for notebook formatting
       - id: black
@@ -60,19 +60,19 @@ repos:
     hooks:
       - id: blacken-docs
         additional_dependencies:
-          - black==23.9.1
+          - black==23.10.1
         # exclude: ^README.md
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.7.0
     hooks:
       - id: nbqa-ruff
-        additional_dependencies: [ruff==0.0.289]
+        additional_dependencies: [ruff==0.1.3]
       - id: nbqa-black
-        additional_dependencies: [black==23.9.1]
+        additional_dependencies: [black==23.10.1]
 
   # * Commit message
   - repo: https://github.com/commitizen-tools/commitizen
-    rev: 3.9.0
+    rev: 3.12.0
     hooks:
       - id: commitizen
         stages: [commit-msg]
@@ -85,7 +85,7 @@ repos:
       - id: isort
         stages: [manual]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+    rev: v3.15.0
     hooks:
       - id: pyupgrade
         stages: [manual]
@@ -113,7 +113,7 @@ repos:
         stages: [manual]
   # ** spelling
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
         types_or: [python, rst, markdown, cython, c]

CHANGELOG.md

@@ -1,16 +1,36 @@
 <!-- markdownlint-disable MD024 -->
+<!-- markdownlint-disable MD013 -->
+<!-- prettier-ignore-start -->
 
 # Changelog
 
 Changelog for `pyproject2conda`
 
 ## Unreleased
 
-See the fragment files in
-[changelog.d](https://github.com/usnistgov/pyproject2conda)
+[changelog.d]: https://github.com/usnistgov/pyproject2conda/tree/main/changelog.d
+
+See the fragment files in [changelog.d]
+
+<!-- prettier-ignore-end -->
+
+<!-- markdownlint-enable MD013 -->
 
 <!-- scriv-insert-here -->
 
+## v0.9.0 — 2023-11-14
+
+### Added
+
+- Default is now to remove whitespace from dependencies. For example, the
+  dependency `module > 0.1` will become `module>0.1`. To override this
+  behaviour, pass the option `--no-remove-whitespace`.
+- Now supports python version `>3.8,<=3.12`
+- Can now specify `extras = false` in pyprojec.toml to skip any extras. The
+  default (`extras = true`) is the same as `extras = [env_name]` where
+  `env_name` is the name of the environment (e.g.,
+  `tool.pyproject2conda.envs.env_name`).
+
 ## v0.8.0 — 2023-10-02
 
 ### Added

CONTRIBUTING.md

@@ -7,7 +7,9 @@ You can contribute in many ways:
 
 ## Types of Contributions
 
+<!-- prettier-ignore-start -->
 [issues]: https://github.com/usnistgov/pyproject2conda/issues
+<!-- prettier-ignore-end -->
 
 ### Report Bugs
 
@@ -31,9 +33,9 @@ and "help wanted" is open to whoever wants to implement it.
 
 ### Write Documentation
 
-`pyproject2conda` could always use more documentation, whether as part of the
-official `pyproject2conda` docs, in docstrings, or even on the web in blog
-posts, articles, and such.
+This project could always use more documentation, whether as part of the
+official docs, in docstrings, or even on the web in blog posts, articles, and
+such.
 
 ### Submit Feedback
 
@@ -48,10 +50,9 @@ If you are proposing a feature:
 
 ## Making a contribution
 
-Ready to contribute? Here's how to set up `pyproject2conda` for local
-development.
+Ready to contribute? Here's how to make a contribution.
 
-- Fork the `pyproject2conda` repo on GitHub.
+- Fork the repo on GitHub.
 
 - Clone your fork locally:
 
@@ -278,6 +279,8 @@ where commands can be one of:
   [ghp-import](https://github.com/c-w/ghp-import))
 - livehtml : Live documentation updates
 - open : open the documentation in a web browser
+- serve : Serve the created documentation webpage (Need this to view javescript
+  in created pages).
 
 ## Testing with nox
 
@@ -517,22 +520,23 @@ Before you submit a pull request, check that it meets these guidelines:
 
 [setuptools_scm]: https://github.com/pypa/setuptools_scm
 
-Versioning is handled with [setuptools_scm].The package version is set by the
+Versioning is handled with [setuptools_scm]. The package version is set by the
 git tag. For convenience, you can override the version with nox setting
 `--version ...`. This is useful for updating the docs, etc.
 
-We use the `write_to` option to [setuptools_scm]. This stores the current
-version in `_version.py`. Note that if you build the package (or, build docs
-with the `--version` flag), this will overwrite information in `_version.py` in
-the `src` directory. To refresh the version, run:
+Note that the version in a given environment/session can become stale. The
+easiest way to update the installed package version version is to reinstall the
+package. This can be done using the following:
 
 ```bash
-make version-scm
+pip install -e . --no-deps
 ```
 
-Note also that the file `_version.py` SHOULD NOT be tracked by git. It will be
-autogenerated when building the package. This scheme avoids having to install
-`setuptools-scm` (and `setuptools`) in each environment.
+To do this in a given session, use:
+
+```bash
+nox -s {session} -- -P/--update-package
+```
 
 ## Serving the documentation
 
@@ -542,4 +546,9 @@ To view to documentation with js headers/footers, you'll need to serve them:
 python -m http.server -d docs/_build/html
 ```
 
-Then open the address `localhost:8000` in a webbrowser.
+Then open the address `localhost:8000` in a webbrowser. Alternatively, you can
+run:
+
+```bash
+nox -s docs -- -d serve
+```

Makefile

@@ -141,6 +141,9 @@ version-scm: ## check/update version of package with setuptools-scm
 version-import: ## check version from python import
 	-python -c 'import pyproject2conda; print(pyproject2conda.__version__)'
 
+version-update: ## update version using nox
+	nox -s update-version-scm
+
 version: version-scm version-import
 
 ################################################################################
@@ -149,9 +152,10 @@ version: version-scm version-import
 .PHONY: requirements
 requirements: ## rebuild all requirements/environment files
 	nox -s requirements
-
-requirements/%.yaml: pyproject.toml requirements
-requirements/%.txt: pyproject.toml requirements
+requirements/%.yaml: pyproject.toml
+	nox -s requirements
+requirements/%.txt: pyproject.toml
+	nox -s requirements
 
 ################################################################################
 # * NOX
@@ -283,7 +287,8 @@ pytest-nbval:  ## run pytest --nbval
 
 .PHONY: cog-readme
 cog-readme: ## apply cog to README.md
-	P2C_COLUMNS=100 cog -rP README.md
+	# P2C_COLUMNS=100 cog -rP README.md
+	nox -s cog
 	pre-commit run markdownlint --files README.md
 
 # NOTE: Some special stuff for README.pdf

README.md

@@ -507,6 +507,18 @@ python = ["3.10"]
 user_config = "config/userconfig.toml"
 default_envs = ["test", "dev", "dist-pypi"]
 
+[tool.pyproject2conda.envs.base]
+style = ["requirements"]
+# Note that the default value for `extras` is the name of the environment.
+# To have no extras, either pass
+# extras = []
+# or
+#
+extras = false
+
+#
+# A value of `extras = true` also implies using the environment name
+# as the extras.
 [tool.pyproject2conda.envs."test-extras"]
 extras = ["test"]
 style = ["yaml", "requirements"]
@@ -610,6 +622,18 @@ python = ["3.10"]
 user_config = "config/userconfig.toml"
 default_envs = ["test", "dev", "dist-pypi"]
 
+[tool.pyproject2conda.envs.base]
+style = ["requirements"]
+# Note that the default value for `extras` is the name of the environment.
+# To have no extras, either pass
+# extras = []
+# or
+#
+extras = false
+
+#
+# A value of `extras = true` also implies using the environment name
+# as the extras.
 [tool.pyproject2conda.envs."test-extras"]
 extras = ["test"]
 style = ["yaml", "requirements"]
@@ -629,11 +653,16 @@ python = ["3.10", "3.11"]
 run through the command `pyproject2conda project` (or `p2c project`):
 
 <!-- markdownlint-disable-next-line MD013 -->
-<!-- [[[cog run_command("p2c project -f tests/data/test-pyproject.toml --dry", wrapper="bash", bounds=(None, 45))]]] -->
+<!-- [[[cog run_command("p2c project -f tests/data/test-pyproject.toml --dry ", wrapper="bash", bounds=(None, 45))]]] -->
 
 ```bash
 $ p2c project -f tests/data/test-pyproject.toml --dry
 # --------------------
+# Creating requirements base.txt
+athing
+bthing
+cthing;python_version<'3.10'
+# --------------------
 # Creating yaml py310-test-extras.yaml
 channels:
   - conda-forge
@@ -673,11 +702,6 @@ dependencies:
   - python=3.11
   - bthing-conda
   - conda-forge::pytest
-  - pandas
-  - pip
-  - pip:
-      - athing
-# --------------------
 
  ...
 ```

docs/conf.py

@@ -58,7 +58,6 @@
     # "sphinx_design"
     ## myst stuff
     "myst_nb",
-    # project specific
     "sphinx_click",
 ]
 
@@ -114,7 +113,10 @@
 # nb_execution_mode = "auto"
 
 # set the kernel name
-nb_kernel_rgx_aliases = {"pyproject2conda.*": "python3", "conda.*": "python3"}
+nb_kernel_rgx_aliases = {
+    "pyproject2conda.*": "python3",
+    "conda.*": "python3",
+}
 
 nb_execution_allow_errors = True
 
@@ -478,7 +480,9 @@ def linkcode_resolve(domain, info):
     else:
         linespec = ""
 
+    # fmt: off
     fn = os.path.relpath(fn, start=os.path.dirname(pyproject2conda.__file__))
+    # fmt: on
 
     return f"https://github.com/{github_username}/pyproject2conda/blob/{html_context['github_version']}/src/pyproject2conda/{fn}{linespec}"