Merge branch 'release/v0.6.0'

usnistgov · Sep 20, 2023 · 86a5fad · 86a5fad
2 parents 7241807 + a3d57fc
commit 86a5fad
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diff --git a/.cruft.json b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/wpk-nist-gov/cookiecutter-pypackage.git",
-  "commit": "33236949f71e1d4dad788b8e98fa07716799825e",
+  "commit": "c58ff2e325176899b92f4fbd56584aa0ca478919",
   "checkout": "feature/nox",
   "context": {
     "cookiecutter": {

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
@@ -7,7 +6,7 @@ default_install_hook_types:
   - pre-commit
   - commit-msg
 repos:
-  #* Top level
+  # * Top level
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
@@ -19,79 +18,67 @@ repos:
       - id: check-merge-conflict
       - id: check-symlinks
       - id: check-toml
-  #* Formatting
+  # * sync dependencies
+  # Put this first, because messes up formatting
+  - repo: https://github.com/mxr/sync-pre-commit-deps
+    rev: v0.0.1
+    hooks:
+      - id: sync-pre-commit-deps
+
+  # * Prettier
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v3.0.3"
     hooks:
       - id: prettier
+        alias: markdownlint
         stages: [commit]
         additional_dependencies:
           - prettier-plugin-toml
-        exclude: ^environment/lock/.*[.]yaml
-  #** markdown
+        exclude: ^environment/lock/.*[.]yml
+
+  # * Markdown
   - repo: https://github.com/DavidAnson/markdownlint-cli2
     rev: v0.9.2
     hooks:
       - id: markdownlint-cli2
+        alias: markdownlint
         args: ["--style prettier"]
-  #* Linting
+
+  # * Linting
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     # Ruff version.
-    rev: "v0.0.287"
+    rev: "v0.0.289"
     hooks:
       - id: ruff
   - repo: https://github.com/psf/black
-    rev: 23.9.0
+    rev: 23.9.1
     hooks:
-      # - id: black-jupyter
-      # Move to just black.  use nbqa for notebook formatting
+      # NOTE: nbQA for notebook formatting
       - id: black
   - repo: https://github.com/adamchainz/blacken-docs
     rev: "1.16.0"
     hooks:
       - id: blacken-docs
         additional_dependencies:
-          - black==23.9.0
+          - black==23.9.1
         # exclude: ^README.md
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.7.0
     hooks:
       - id: nbqa-ruff
-        additional_dependencies: [ruff]
+        additional_dependencies: [ruff==0.0.289]
       - id: nbqa-black
-        additional_dependencies: [black]
+        additional_dependencies: [black==23.9.1]
 
-  #* Commit message
+  # * Commit message
   - repo: https://github.com/commitizen-tools/commitizen
-    rev: 3.8.1
+    rev: 3.9.0
     hooks:
       - id: commitizen
         stages: [commit-msg]
 
-  #* Manual Linting
-  - repo: local
-    hooks:
-      - id: mypy
-        name: mypy
-        entry: tox
-        args: ["-e", "lint-mypy"]
-        language: system
-        pass_filenames: false
-        # additional_dependencies: [tox]
-        types: [python]
-        require_serial: true
-        stages: [manual]
-      - id: pyright
-        name: pyright
-        entry: pyright
-        args: []
-        language: system
-        pass_filenames: true
-        # additional_dependencies: [tox]
-        types: [python]
-        require_serial: true
-        stages: [manual]
-  # isort, pyupgrade, flake8 defer to ruff
+  # * Manual Linting ------------------------------------------------------------
+  # * isort, pyupgrade, flake8 defer to ruff
   - repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks:
@@ -124,7 +111,7 @@ repos:
       - id: nbqa-isort
         additional_dependencies: [isort]
         stages: [manual]
-  #** spelling
+    # ** spelling
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.5
     hooks:
@@ -133,3 +120,26 @@ repos:
         additional_dependencies: [tomli]
         args: [-I, docs/spelling_wordlist.txt]
         stages: [manual]
+
+  # - repo: local
+  #   hooks:
+  #     - id: mypy
+  #       name: mypy
+  #       entry: tox
+  #       args: ["-e", "lint-mypy"]
+  #       language: system
+  #       pass_filenames: false
+  #       # additional_dependencies: [tox]
+  #       types: [python]
+  #       require_serial: true
+  #       stages: [manual]
+  #     - id: pyright
+  #       name: pyright
+  #       entry: pyright
+  #       args: []
+  #       language: system
+  #       pass_filenames: true
+  #       # additional_dependencies: [tox]
+  #       types: [python]
+  #       require_serial: true
+  #       stages: [manual]
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,11 +11,22 @@ See the fragment files in
 
 <!-- scriv-insert-here -->
 
+## v0.6.0 — 2023-09-19
+
+### Added
+
+- Added `project` subcommand. This uses a configuration in `pyproject.toml` to
+  build multiple enivonments in one go.
+- Added `--deps` and `--reqs` flags to include extra conda and pip requirements.
+- Added `--overwrite` to check if output file exists.
+- Now (correctly) using rich_click.
+- Added tests for all new cases, and some edge cases.
+
 ## v0.5.1 — 2023-09-09
 
 ### Added
 
-- Added `--sort/--no-sort` flag to cli. Default is to sort dependecies. This
+- Added `--sort/--no-sort` flag to cli. Default is to sort dependencies. This
   fixes issues with changing order in `pyproject.toml` leading to different yaml
   files.
 

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -188,7 +188,7 @@ the search path, and the development environment will include the extras `dev`
 and `nox` from the `project.optional-dependencies` section of the
 `pyproject.toml` file in the development environment.
 
-You can alos create this file using either of the following commands:
+You can also create this file using either of the following commands:
 
 ```bash
 nox -s config -- --python-paths "~/.conda/envs/test-3.*/bin" --dev-extras dev nox...
@@ -211,6 +211,28 @@ done
 
 Also, set the variable `nox.python.paths` (see [](#setup-user-configuration)).
 
+### See nox sessions/options
+
+To see all nox session, run:
+
+```bash
+nox --list
+```
+
+We use [noxopt] to pass command line options to the different sessions. Use the
+following to get help on these options:
+
+```bash
+nox -- --help
+```
+
+Note that these options should be passed _after_ `--`. For example, to build and
+open the documentation, run:
+
+```bash
+nox -s docs -- -d build open
+```
+
 ### Creating environment.yaml/requirement.txt files
 
 The project is setup to create `environemt.yaml` and `requirement.txt` files
@@ -367,25 +389,36 @@ pipx run --spec git+https://github.com/wpk-nist-gov/nox-bootstrap.git \
      nox -s bootstrap -- \
      --python-paths "~/.conda/envs/test-3.*/bin" \
      --dev-extras dev nox
-```
 
-This will, in isolation, install nox, and run the `bootstrap` session.
+conda activate .nox/{project-name}/envs/dev
+```
 
-The above commands create a development environment located at
-`.nox/{project-name}/envs/dev`.
+where options `--python-paths` and `--dev-extras` are user specific. This will,
+in isolation, install nox, and run the `bootstrap` session.
 
 Note that nox environments are under `.nox/{project-name}/envs` instead of under
 `.nox`. This fixes some issues with things like [nb_conda_kernels], as well as
 other third party tools that expect conda environment to be located in a
 directory like `.../miniforge/envs/env-name`.
 
+If you go this route, you may want to use something like
+[zsh-autoenv](https://github.com/Tarrasch/zsh-autoenv) (if using zsh shell) or
+[autoenv](https://github.com/hyperupcall/autoenv) (if using bash) to auto
+activate the development environment when in the parent directory.
+
+### Conda create development environment
+
 If instead you'd like to just install directly with conda, you can use:
 
 ```bash
-conda env create [-n {env-name}] -f environment/py{version}-dev-base.yaml
-conda activate {environment-name or -p path/to/environment}
+conda env create [-n {env-name}] -f environment/py{version}-dev-complete.yaml
+conda activate {env-name}
+pip install -e . --no-deps
 ```
 
+This installs all optional dependencies except those need to build the docs. For
+that, please use nox.
+
 ### Development tools
 
 [pipx]: https://github.com/pypa/pipx
@@ -406,16 +439,20 @@ conda activate {environment-name or -p path/to/environment}
 [nb_conda_kernels]: https://github.com/Anaconda-Platform/nb_conda_kernels
 [pyproject2conda]: https://github.com/usnistgov/pyproject2conda
 [nbqa]: https://github.com/nbQA-dev/nbQA
+[pyright]: https://github.com/microsoft/pyright
 
 We recommend installing the following tools with [pipx] or [condax]. If you'd
 like to install them in the development environment instead, include the
 "extras" `tools` in the `nox.extras.dev` section of `config/userconfig.toml`
-file:
+file, or run:
 
 ```bash
 nox -s config -- --dev-extras dev nox tools
 ```
 
+Alternatively, you can just create a conda environment using the commands in
+[](#conda-create-development-environment).
+
 Additional tools are:
 
 - [pre-commit]
@@ -426,6 +463,7 @@ Additional tools are:
 - [pyproject2conda] (optional)
 - [cog] (optional)
 - [nbqa] (optional)
+- [pyright] (recommended)
 
 These are setup using the following:
 
@@ -438,6 +476,7 @@ pipx install scriv
 condax/pipx install commitizen
 condax/pipx install cogapp
 condax/pipx install nbqa
+condax/pipx install pyright
 ```
 
 If you'd like to install a central [nox] to be used with this project, use one

diff --git a/Makefile b/Makefile
@@ -295,3 +295,4 @@ pytest-nbval:  ## run pytest --nbval
 .PHONY: cog-readme
 cog-readme: ## apply cog to README.md
 	cog -rP README.md
+	pre-commit run markdownlint --files README.md