Fix docs template so that it builds

containers/test-template/test-template.sh

@@ -10,14 +10,11 @@ script="'${script_name}' tests/data tests/result participant -c1 --skip-bids-val
 case "$method" in
     "setuptools" )
         python -m venv .venv
-        .venv/bin/python -m pip install .
-        # if [ -d /src ]; then
-        #     .venv/bin/python -m pip install /src
-        # fi
+        .venv/bin/python -m pip install --no-color .
         PATH=".venv/bin:$PATH" eval "$script"
         ;;
     "poetry" )
-        poetry install
+        poetry install --no-ansi
         eval "poetry run $script"
         ;;
     "hatch" )
@@ -28,6 +25,12 @@ case "$method" in
         pdm install
         eval "pdm run $script"
         ;;
+    "docs" )
+        python -m venv .venv
+        .venv/bin/python -m pip install .
+        .venv/bin/python -m pip install -r docs/requirements.txt
+        .venv/bin/sphinx-build docs build/docs -W
+        ;;
     * )
         >&2 echo "Invalid method"
         exit 1

snakebids/project_template/.gitignore

@@ -0,0 +1,160 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

snakebids/project_template/{% if create_doc_template %}docs{% endif %}/conf.py.jinja

@@ -30,6 +30,7 @@ author = "{{full_name}}"
 extensions = [
     "sphinx_rtd_theme",
     "sphinxarg.ext",
+    "myst_parser",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -54,4 +55,4 @@ html_theme = "sphinx_rtd_theme"
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+# html_static_path = ["_static"]

snakebids/project_template/{% if create_doc_template %}docs{% endif %}/getting_started/installation.md.jinja

@@ -1,4 +1,4 @@
-## Installation
+# Installation
 
 Install from github with pip:
 
@@ -8,7 +8,7 @@ pip install -e git+https://github.com/{{github}}/{{name_slug}}#egg={{name_slug}}
 
 Note: you can re-run this command to re-install with the latest version
 
-## Running the app
+# Running the app
 
 Do a dry-run first (`-n`) and simply print (`-p`) what would be run:
 
@@ -24,7 +24,7 @@ Run the app, using all cores::
 
 If any workflow rules require containers, then run with the `--use-singularity` option.
 
-## Generating a report
+# Generating a report
 
 After your processing is complete, you can use snakemake's `--report` feature to generate
 an HTML report. This report will include a graph of all the jobs run, with clickable nodes
@@ -38,13 +38,13 @@ To generate a report, run:
 {{name_slug}} /path/to/bids/dir /path/to/output/dir participant --report
 ```
 
-## Compute Canada Instructions
+# Compute Canada Instructions
 
-### Setting up a dev environment
+## Setting up a dev environment
 
 Here are some instructions to get your python environment set-up on graham to run {{name_slug}}:
 
-# Create a virtualenv and activate it:
+### Create a virtualenv and activate it:
 
 ```bash
 cd $SCRATCH
@@ -53,9 +53,9 @@ virtualenv venv_{{name_slug}}
 source venv_{{name_slug}}/bin/activate
 ```
 
-# Follow the steps above to install from github repository
+### Follow the steps above to install from github repository
 
-### Install job submission helpers
+## Install job submission helpers
 
 Snakemake can submit jobs with SLURM, but you need to set-up a Snakemake profile to enable this. The Khan lab has a
 snakemake profile that is configured for graham but is customizable upon install, please see `cc-slurm <https://github.com/khanlab/cc-slurm>` for more info.
@@ -64,7 +64,7 @@ If you don't need Snakemake to parallelize jobs across different nodes, you can
 
 These are used in the instructions below.
 
-### Running jobs on Compute Canada
+## Running jobs on Compute Canada
 
 In an interactive job (for testing):
 

snakebids/project_template/{% if create_doc_template %}docs{% endif %}/index.md

@@ -4,7 +4,7 @@
 
 ```{toctree}
 :maxdepth: 1
-:caption: Contents:
+:caption: "Contents:"
 ```
 
 ```{toctree}

snakebids/project_template/{% if create_doc_template %}docs{% endif %}/requirements.txt.jinja

@@ -1,4 +1,4 @@
 docutils<0.18
 sphinx-argparse
 sphinx_rtd_theme
-snakebids=={{ snakebids_version }}
+myst-parser

snakebids/project_template/{% if create_doc_template %}docs{% endif %}/usage/app_cli.md.jinja

@@ -1,7 +1,6 @@
-## Command line interface
+# Command line interface
 
 ```{argparse}
-:filename: ../{{ name_slug }}/run.py
-:func: get_parser
+:ref: {{ name_slug }}.run.get_parser
 :prog: {{ name_slug }}
 ```

snakebids/project_template/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md

@@ -1,4 +1,4 @@
-## Snakemake Command line interface
+# Snakemake Command line interface
 
 ```{argparse}
 :module: snakemake

snakebids/project_template/{{name_slug}}/run.py.jinja → snakebids/project_template/{{name_slug}}/run.py

@@ -6,12 +6,13 @@
 
 
 def get_parser():
-    """Exposes parser for sphinx doc generation, cwd is the docs dir"""
-    app = SnakeBidsApp("../{{ name_slug }}")
+    """Exposes parser for sphinx doc generation, cwd is the docs dir."""
+    app = SnakeBidsApp(Path(__file__).resolve().parent)  # to get repository root
     return app.parser
 
 
 def main():
+    """Run the app."""
     app = SnakeBidsApp(
         Path(__file__).resolve().parent,  # to get repository root
         plugins=[BidsValidator()],

snakebids/tests/helpers.py

@@ -289,14 +289,18 @@ def decorator(func: Callable[_P, _T]) -> Callable[_P, _T]:
         @ft.wraps(func)
         def wrapper(*args: _P.args, **kwargs: _P.kwargs):
             try:
-                sp.run(["docker"], check=True)
+                sp.run(["docker"], check=True, capture_output=True)
             except (sp.CalledProcessError, FileNotFoundError):
                 pytest.fail(
                     "docker is not available on this machine. To skip docker tests, "
                     "use '-m \"not docker\"'"
                 )
             try:
-                sp.run(["docker", "image", "inspect", container], check=True)
+                sp.run(
+                    ["docker", "image", "inspect", container],
+                    capture_output=True,
+                    check=True,
+                )
             except sp.CalledProcessError as err:
                 if not (
                     match := re.match(r"snakebids/([\w\-]+)\:[a-zA-Z0-9\-]+", container)