Fix formatting

.github/pull_request_template.md

@@ -6,4 +6,4 @@
 
 - [ ] This PR is meant for the `lincc-frameworks/python-project-template` repo and not a downstream one instead.
 - [ ] This change is linked to an open issue
-- [ ] This change includes integration testing, or is small enough to be covered by existing tests
+- [ ] This change includes integration testing, or is small enough to be covered by existing tests

.github/workflows/pre-commit-ci.yml

@@ -39,4 +39,4 @@ jobs:
       env:
         SKIP: "check-lincc-frameworks-template-version,no-commit-to-branch,check-added-large-files,validate-pyproject,sphinx-build,pytest-check"
     - uses: pre-commit-ci/lite-action@062bca0919bc9d6e66755cc05074b70c77e111fc  # v1.2.0
-      if: failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false
+      if: failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false

.github/workflows/smoke-test.yml

@@ -82,4 +82,4 @@ jobs:
                 }
               }
             ]
-          }
+          }

.github/workflows/testing-and-coverage.yml

@@ -40,4 +40,4 @@ jobs:
     - name: Run unit tests with pytest /  pytest-copie
       run: |
         git config --global init.defaultBranch main
-        python -m pytest tests -o log_cli=true -vv --python_version ${{ matrix.python-version }}
+        python -m pytest tests -o log_cli=true -vv --python_version ${{ matrix.python-version }}

.setup_dev.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# Bash Unofficial strict mode (http://redsymbol.net/articles/unofficial-bash-strict-mode/) 
+# Bash Unofficial strict mode (http://redsymbol.net/articles/unofficial-bash-strict-mode/)
 # and (https://disconnected.systems/blog/another-bash-strict-mode/)
 set -o nounset # Any uninitialized variable is an error
 set -o errexit # Exit the script on the failure of any command to execute without error

CITATION.bib

@@ -13,4 +13,3 @@ @ARTICLE{2024RNAAS...8..141O
        adsurl = {https://ui.adsabs.harvard.edu/abs/2024RNAAS...8..141O},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
-

copier.yml

@@ -49,7 +49,7 @@ package_name:
 
 project_organization:
     type: str
-    help: What github organization will your project live under? 
+    help: What github organization will your project live under?
     default: my-organization
     validator: >-
         {% if not (project_organization | regex_search('^[a-zA-Z0-9][a-zA-Z0-9-]*$')) %}

docs/Makefile

@@ -8,7 +8,7 @@ SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = ../_readthedocs/
 
-.PHONY: help clean Makefile 
+.PHONY: help clean Makefile
 
 # Put it first so that "make" without argument is like "make help".
 help:
@@ -23,4 +23,3 @@ clean:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-

docs/index.rst

@@ -54,4 +54,3 @@ please :doc:`/source/contact`
    practices/publishing_package
    practices/customizing_project
    practices/development_guide
-

docs/practices/ci_testing.rst

@@ -144,4 +144,4 @@ In your project repo create a new repo secret:
 There is a stage in the end of the ``smoke_test.yml`` file that will
 send failure alerts to the slack channel.
 
-An example can be found in the `rail project <https://github.com/LSSTDESC/rail/blob/main/.github/workflows/smoke-test.yml#L45-L82>`_
+An example can be found in the `rail project <https://github.com/LSSTDESC/rail/blob/main/.github/workflows/smoke-test.yml#L45-L82>`_

docs/practices/conda.rst

@@ -40,4 +40,4 @@ from your repository as normal.
 
 conda-forge periodically looks at your source repo for any new releases/tags, 
 tries to build a new release, and pre-generates the PR (against your "feedstock"
-repo created above) to publish the new version of the package.
+repo created above) to publish the new version of the package.

docs/practices/overview.rst

@@ -24,4 +24,4 @@ Practices
 Still have questions?
 --------------------------------
 
-:doc:`/source/contact`
+:doc:`/source/contact`

docs/practices/pipx.rst

@@ -47,4 +47,4 @@ An example installation of ``pipx`` might look like this.
         >> pipx ensurepath
 
 .. important::
-    Don't forget to run ``pipx ensurepath`` to finalize the installation.
+    Don't forget to run ``pipx ensurepath`` to finalize the installation.

docs/practices/pypi.rst

@@ -38,4 +38,4 @@ Releasing new versions
 
 Now, when you 
 `create a new release <https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository#creating-a-release>`_ 
-from your repository, a workflow will run that will package and deploy the code to PyPI.
+from your repository, a workflow will run that will package and deploy the code to PyPI.

docs/practices/pytest_timing.rst

@@ -131,4 +131,4 @@ Profiling the same target as above, using ``py-spy`` might look like:
 
 You will get a profiling flame chart saved to ``profile.svg``. These are not as
 easy to read as some other flame charts, but they're better than sifting through the
-raw results!
+raw results!

docs/practices/unit_testing.rst

@@ -43,4 +43,4 @@ supports tests embedded in documentation using pytest's
 `doctest <https://doc.pytest.org/en/latest/how-to/doctest.html>`_ component. 
 Documentation comments in all source files, as well as ``.rst`` files in the ``./docs`` 
 directory can contain doctests in the format outlined 
-`here <https://doc.pytest.org/en/latest/how-to/doctest.html>`_.
+`here <https://doc.pytest.org/en/latest/how-to/doctest.html>`_.

docs/requirements.txt

@@ -2,4 +2,4 @@
 sphinx
 sphinx-autoapi
 sphinx-copybutton
-sphinx-rtd-theme>=3.1.0
+sphinx-rtd-theme>=3.1.0

docs/source/citation.rst

@@ -19,4 +19,4 @@ If you use Python Project Template in your work, we ask the you cite the `"A Pyt
         doi = {10.3847/2515-5172/ad4da1},
         adsurl = {https://ui.adsabs.harvard.edu/abs/2024RNAAS...8..141O},
         adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-    }
+    }

docs/source/configuration_checklist.rst

@@ -64,4 +64,4 @@ Get the most out of this template
 Still have questions?
 -------------------------------------------------------------------------------
 
-:doc:`/source/contact`
+:doc:`/source/contact`

docs/source/contributing.rst

@@ -59,4 +59,4 @@ for doing so are here.
 Use your best judgement when incrementing the version. i.e. is this a major,
 minor, or patch fix.
 
-Do you want to help out, but you're not sure how? :doc:`/source/contact`
+Do you want to help out, but you're not sure how? :doc:`/source/contact`

docs/source/existing_project.rst

@@ -237,4 +237,4 @@ to conclude the setup.
 Still have questions?
 ----------------------------------------
 
-:doc:`/source/contact`
+:doc:`/source/contact`

docs/source/overview.rst

@@ -74,4 +74,4 @@ Now choose your next adventure...
 -------------------------------------
 * :doc:`Start a new project<new_project>`
 * :doc:`Configure a new project<configuration_checklist>`
-* :doc:`Upgrade an existing project<existing_project>`
+* :doc:`Upgrade an existing project<existing_project>`

pyproject.toml

@@ -69,4 +69,4 @@ profile = "black"
 line_length = 110
 
 [tool.pytest.ini_options]
-log_cli_level = "INFO"
+log_cli_level = "INFO"

python-project-template/.github/ISSUE_TEMPLATE/README.md

@@ -6,4 +6,4 @@ removing, and modifying these templates to suit the needs of your project is enc
 
 For more information about these templates, look here: https://lincc-ppt.readthedocs.io/en/latest/practices/issue_pr_templating.html
 
-Or if you still have questions contact us: https://lincc-ppt.readthedocs.io/en/latest/source/contact.html
+Or if you still have questions contact us: https://lincc-ppt.readthedocs.io/en/latest/source/contact.html

python-project-template/.github/pull_request_template.md

@@ -1,5 +1,5 @@
 ## Change Description
-<!--- 
+<!---
 Closes #???
 -->
 

python-project-template/.github/workflows/{% if contains_code %}smoke-test.yml{% endif %}.jinja

@@ -46,9 +46,9 @@ jobs:
         pip list
     - name: Run unit tests with pytest
       run: |
-        python -m pytest -o log_cli=true -vv 
+        python -m pytest -o log_cli=true -vv
 {%- if 'email' in failure_notification %}
-    - name: Send status to author's email      
+    - name: Send status to author's email
       if: {% raw %}${{ failure() }} && github.event_name != 'workflow_dispatch' }}{% endraw %} # Only email if the workflow failed and was not manually started. Customize this as necessary.
       uses: dawidd6/action-send-mail@67ce3558d613188179559c61d3565140cf389968  # v22
       with:

python-project-template/.initialize_new_project.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# Bash Unofficial strict mode (http://redsymbol.net/articles/unofficial-bash-strict-mode/) 
+# Bash Unofficial strict mode (http://redsymbol.net/articles/unofficial-bash-strict-mode/)
 # and (https://disconnected.systems/blog/another-bash-strict-mode/)
 set -o nounset # Any uninitialized variable is an error
 set -o errexit # Exit the script on the failure of any command to execute without error

python-project-template/.pre-commit-config.yaml.jinja

@@ -109,7 +109,7 @@ repos:
     rev: 44b5042edab9382aba712eed4f9c7bab7a3d6a3e  # v0.17.0
     hooks:
       - id: ruff
-        name: Lint code using ruff; sort and organize imports 
+        name: Lint code using ruff; sort and organize imports
         types_or: [ python, pyi ]
         args: ["--fix"]
 {%- endif %}

python-project-template/{% if include_benchmarks %}benchmarks{% endif %}/README.md

@@ -9,4 +9,4 @@ tracked and reported to give you a sense of the overall performance of your code
 You are encouraged to add, update, or remove benchmark functions to suit the needs
 of your project.
 
-For more information, see the documentation here: https://lincc-ppt.readthedocs.io/en/latest/practices/ci_benchmarking.html
+For more information, see the documentation here: https://lincc-ppt.readthedocs.io/en/latest/practices/ci_benchmarking.html

python-project-template/{% if include_benchmarks %}benchmarks{% endif %}/asv.conf.json.jinja

@@ -78,4 +78,4 @@
     //    "some_benchmark": "352cdf",  // Consider regressions only after this commit
     //    "another_benchmark": null,   // Skip regression detection altogether
     // }
-}
+}

python-project-template/{% if include_docs %}docs{% endif %}/Makefile.jinja

@@ -33,4 +33,3 @@ clean:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-

python-project-template/{% if include_docs %}docs{% endif %}/notebooks/README.md

@@ -22,4 +22,4 @@ For notebooks that require large datasets, access to third party APIs, large CPU
 
 For more information look here: https://lincc-ppt.readthedocs.io/en/latest/practices/sphinx.html#python-notebooks
 
-Or if you still have questions contact us: https://lincc-ppt.readthedocs.io/en/latest/source/contact.html
+Or if you still have questions contact us: https://lincc-ppt.readthedocs.io/en/latest/source/contact.html

python-project-template/{% if include_docs %}docs{% endif %}/requirements.txt.jinja

@@ -8,4 +8,4 @@ nbsphinx
 sphinx
 sphinx-autoapi
 sphinx-copybutton
-sphinx-rtd-theme>=3.0
+sphinx-rtd-theme>=3.0

python-versions.jinja

@@ -1,22 +1,22 @@
 {# You use this file by including it via jinja like:
 
-    {%- import 'python-versions.jinja' as py -%} 
+    {%- import 'python-versions.jinja' as py -%}
 
-Then pass the python_versions list into the various macros like so: 
+Then pass the python_versions list into the various macros like so:
 
-  {{ py.min(python_versions) }} 
+  {{ py.min(python_versions) }}
 
-This template creates no output, but does allow you to transform python_versions answer into a 
-number of helpful values for when you need a single python version. 
+This template creates no output, but does allow you to transform python_versions answer into a
+number of helpful values for when you need a single python version.
 
 Note that the import syntax and access MUST BE in the form above. Copier has problems processing import lines
 that are any more complex when they occur in files who's paths are also jinja templated. #}
 
 
-{# This gives a middle python version from a potentially long list of versions 
-For even-length lists we prefer the older of the two middle values. 
-   ["3.9","3.10","3.11","3.12"] -> "3.10" 
-For odd-length lists we prefer the middle value 
+{# This gives a middle python version from a potentially long list of versions
+For even-length lists we prefer the older of the two middle values.
+   ["3.9","3.10","3.11","3.12"] -> "3.10"
+For odd-length lists we prefer the middle value
    ["3.9","3.10","3.11"] -> "3.10"        #}
 {% macro pref(python_versions) -%}
 {%- set n = python_versions | length -%}
@@ -32,4 +32,4 @@ For odd-length lists we prefer the middle value
 {% macro max(python_versions) -%}
 {%- set n = python_versions | length -%}
 {{ python_versions[n-1] }}
-{%- endmacro -%}
+{%- endmacro -%}

tox.ini

@@ -9,4 +9,3 @@ deps =
     pylint
 commands =
     pytest tests
-