SingleCellExperiment 0.2.5__tar.gz → 0.3.0__tar.gz

SingleCellExperiment-0.3.0/.pre-commit-config.yaml

@@ -0,0 +1,67 @@
+exclude: '^docs/conf.py'
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: trailing-whitespace
+  - id: check-added-large-files
+  - id: check-ast
+  - id: check-json
+  - id: check-merge-conflict
+  - id: check-xml
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: requirements-txt-fixer
+  - id: mixed-line-ending
+    args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+
+## If you want to automatically "modernize" your Python code:
+# - repo: https://github.com/asottile/pyupgrade
+#   rev: v3.7.0
+#   hooks:
+#   - id: pyupgrade
+#     args: ['--py37-plus']
+
+## If you want to avoid flake8 errors due to unused vars or imports:
+# - repo: https://github.com/PyCQA/autoflake
+#   rev: v2.1.1
+#   hooks:
+#   - id: autoflake
+#     args: [
+#       --in-place,
+#       --remove-all-unused-imports,
+#       --remove-unused-variables,
+#     ]
+
+- repo: https://github.com/PyCQA/isort
+  rev: 5.12.0
+  hooks:
+  - id: isort
+
+- repo: https://github.com/psf/black
+  rev: 23.7.0
+  hooks:
+  - id: black
+    language_version: python3
+
+## If like to embrace black styles even in the docs:
+# - repo: https://github.com/asottile/blacken-docs
+#   rev: v1.13.0
+#   hooks:
+#   - id: blacken-docs
+#     additional_dependencies: [black]
+
+- repo: https://github.com/PyCQA/flake8
+  rev: 6.1.0
+  hooks:
+  - id: flake8
+  ## You can add flake8 plugins via `additional_dependencies`:
+  #  additional_dependencies: [flake8-bugbear]
+
+## Check for misspells in documentation files:
+# - repo: https://github.com/codespell-project/codespell
+#   rev: v2.2.5
+#   hooks:
+#   - id: codespell

SingleCellExperiment-0.3.0/CONTRIBUTING.md

@@ -0,0 +1,371 @@
+```{todo} THIS IS SUPPOSED TO BE AN EXAMPLE. MODIFY IT ACCORDING TO YOUR NEEDS!
+
+   The document assumes you are using a source repository service that promotes a
+   contribution model similar to [GitHub's fork and pull request workflow].
+   While this is true for the majority of services (like GitHub, GitLab,
+   BitBucket), it might not be the case for private repositories (e.g., when
+   using Gerrit).
+
+   Also notice that the code examples might refer to GitHub URLs or the text
+   might use GitHub specific terminology (e.g., *Pull Request* instead of *Merge
+   Request*).
+
+   Please make sure to check the document having these assumptions in mind
+   and update things accordingly.
+```
+
+```{todo} Provide the correct links/replacements at the bottom of the document.
+```
+
+```{todo} You might want to have a look on [PyScaffold's contributor's guide],
+
+   especially if your project is open source. The text should be very similar to
+   this template, but there are a few extra contents that you might decide to
+   also include, like mentioning labels of your issue tracker or automated
+   releases.
+```
+
+# Contributing
+
+Welcome to `SingleCellExperiment` contributor's guide.
+
+This document focuses on getting any potential contributor familiarized with
+the development processes, but [other kinds of contributions] are also appreciated.
+
+If you are new to using [git] or have never collaborated in a project previously,
+please have a look at [contribution-guide.org]. Other resources are also
+listed in the excellent [guide created by FreeCodeCamp] [^contrib1].
+
+Please notice, all users and contributors are expected to be **open,
+considerate, reasonable, and respectful**. When in doubt,
+[Python Software Foundation's Code of Conduct] is a good reference in terms of
+behavior guidelines.
+
+## Issue Reports
+
+If you experience bugs or general issues with `SingleCellExperiment`, please have a look
+on the [issue tracker].
+If you don't see anything useful there, please feel free to fire an issue report.
+
+:::{tip}
+Please don't forget to include the closed issues in your search.
+Sometimes a solution was already reported, and the problem is considered
+**solved**.
+:::
+
+New issue reports should include information about your programming environment
+(e.g., operating system, Python version) and steps to reproduce the problem.
+Please try also to simplify the reproduction steps to a very minimal example
+that still illustrates the problem you are facing. By removing other factors,
+you help us to identify the root cause of the issue.
+
+## Documentation Improvements
+
+You can help improve `SingleCellExperiment` docs by making them more readable and coherent, or
+by adding missing information and correcting mistakes.
+
+`SingleCellExperiment` documentation uses [Sphinx] as its main documentation compiler.
+This means that the docs are kept in the same repository as the project code, and
+that any documentation update is done in the same way was a code contribution.
+
+```{todo} Don't forget to mention which markup language you are using.
+
+    e.g.,  [reStructuredText] or [CommonMark] with [MyST] extensions.
+```
+
+```{todo} If your project is hosted on GitHub, you can also mention the following tip:
+
+   :::{tip}
+      Please notice that the [GitHub web interface] provides a quick way of
+      propose changes in `SingleCellExperiment`'s files. While this mechanism can
+      be tricky for normal code contributions, it works perfectly fine for
+      contributing to the docs, and can be quite handy.
+
+      If you are interested in trying this method out, please navigate to
+      the `docs` folder in the source [repository], find which file you
+      would like to propose changes and click in the little pencil icon at the
+      top, to open [GitHub's code editor]. Once you finish editing the file,
+      please write a message in the form at the bottom of the page describing
+      which changes have you made and what are the motivations behind them and
+      submit your proposal.
+   :::
+```
+
+When working on documentation changes in your local machine, you can
+compile them using [tox] :
+
+```
+tox -e docs
+```
+
+and use Python's built-in web server for a preview in your web browser
+(`http://localhost:8000`):
+
+```
+python3 -m http.server --directory 'docs/_build/html'
+```
+
+## Code Contributions
+
+```{todo} Please include a reference or explanation about the internals of the project.
+
+   An architecture description, design principles or at least a summary of the
+   main concepts will make it easy for potential contributors to get started
+   quickly.
+```
+
+### Submit an issue
+
+Before you work on any non-trivial code contribution it's best to first create
+a report in the [issue tracker] to start a discussion on the subject.
+This often provides additional considerations and avoids unnecessary work.
+
+### Create an environment
+
+Before you start coding, we recommend creating an isolated [virtual environment]
+to avoid any problems with your installed Python packages.
+This can easily be done via either [virtualenv]:
+
+```
+virtualenv <PATH TO VENV>
+source <PATH TO VENV>/bin/activate
+```
+
+or [Miniconda]:
+
+```
+conda create -n SingleCellExperiment python=3 six virtualenv pytest pytest-cov
+conda activate SingleCellExperiment
+```
+
+### Clone the repository
+
+1. Create an user account on GitHub if you do not already have one.
+
+2. Fork the project [repository]: click on the *Fork* button near the top of the
+   page. This creates a copy of the code under your account on GitHub.
+
+3. Clone this copy to your local disk:
+
+   ```
+   git clone git@github.com:YourLogin/SingleCellExperiment.git
+   cd SingleCellExperiment
+   ```
+
+4. You should run:
+
+   ```
+   pip install -U pip setuptools -e .
+   ```
+
+   to be able to import the package under development in the Python REPL.
+
+   ```{todo} if you are not using pre-commit, please remove the following item:
+   ```
+
+5. Install [pre-commit]:
+
+   ```
+   pip install pre-commit
+   pre-commit install
+   ```
+
+   `SingleCellExperiment` comes with a lot of hooks configured to automatically help the
+   developer to check the code being written.
+
+### Implement your changes
+
+1. Create a branch to hold your changes:
+
+   ```
+   git checkout -b my-feature
+   ```
+
+   and start making changes. Never work on the main branch!
+
+2. Start your work on this branch. Don't forget to add [docstrings] to new
+   functions, modules and classes, especially if they are part of public APIs.
+
+3. Add yourself to the list of contributors in `AUTHORS.rst`.
+
+4. When you’re done editing, do:
+
+   ```
+   git add <MODIFIED FILES>
+   git commit
+   ```
+
+   to record your changes in [git].
+
+   ```{todo} if you are not using pre-commit, please remove the following item:
+   ```
+
+   Please make sure to see the validation messages from [pre-commit] and fix
+   any eventual issues.
+   This should automatically use [flake8]/[black] to check/fix the code style
+   in a way that is compatible with the project.
+
+   :::{important}
+   Don't forget to add unit tests and documentation in case your
+   contribution adds an additional feature and is not just a bugfix.
+
+   Moreover, writing a [descriptive commit message] is highly recommended.
+   In case of doubt, you can check the commit history with:
+
+   ```
+   git log --graph --decorate --pretty=oneline --abbrev-commit --all
+   ```
+
+   to look for recurring communication patterns.
+   :::
+
+5. Please check that your changes don't break any unit tests with:
+
+   ```
+   tox
+   ```
+
+   (after having installed [tox] with `pip install tox` or `pipx`).
+
+   You can also use [tox] to run several other pre-configured tasks in the
+   repository. Try `tox -av` to see a list of the available checks.
+
+### Submit your contribution
+
+1. If everything works fine, push your local branch to the remote server with:
+
+   ```
+   git push -u origin my-feature
+   ```
+
+2. Go to the web page of your fork and click "Create pull request"
+   to send your changes for review.
+
+   ```{todo} if you are using GitHub, you can uncomment the following paragraph
+
+      Find more detailed information in [creating a PR]. You might also want to open
+      the PR as a draft first and mark it as ready for review after the feedbacks
+      from the continuous integration (CI) system or any required fixes.
+
+   ```
+
+### Troubleshooting
+
+The following tips can be used when facing problems to build or test the
+package:
+
+1. Make sure to fetch all the tags from the upstream [repository].
+   The command `git describe --abbrev=0 --tags` should return the version you
+   are expecting. If you are trying to run CI scripts in a fork repository,
+   make sure to push all the tags.
+   You can also try to remove all the egg files or the complete egg folder, i.e.,
+   `.eggs`, as well as the `*.egg-info` folders in the `src` folder or
+   potentially in the root of your project.
+
+2. Sometimes [tox] misses out when new dependencies are added, especially to
+   `setup.cfg` and `docs/requirements.txt`. If you find any problems with
+   missing dependencies when running a command with [tox], try to recreate the
+   `tox` environment using the `-r` flag. For example, instead of:
+
+   ```
+   tox -e docs
+   ```
+
+   Try running:
+
+   ```
+   tox -r -e docs
+   ```
+
+3. Make sure to have a reliable [tox] installation that uses the correct
+   Python version (e.g., 3.7+). When in doubt you can run:
+
+   ```
+   tox --version
+   # OR
+   which tox
+   ```
+
+   If you have trouble and are seeing weird errors upon running [tox], you can
+   also try to create a dedicated [virtual environment] with a [tox] binary
+   freshly installed. For example:
+
+   ```
+   virtualenv .venv
+   source .venv/bin/activate
+   .venv/bin/pip install tox
+   .venv/bin/tox -e all
+   ```
+
+4. [Pytest can drop you] in an interactive session in the case an error occurs.
+   In order to do that you need to pass a `--pdb` option (for example by
+   running `tox -- -k <NAME OF THE FALLING TEST> --pdb`).
+   You can also setup breakpoints manually instead of using the `--pdb` option.
+
+## Maintainer tasks
+
+### Releases
+
+```{todo} This section assumes you are using PyPI to publicly release your package.
+
+   If instead you are using a different/private package index, please update
+   the instructions accordingly.
+```
+
+If you are part of the group of maintainers and have correct user permissions
+on [PyPI], the following steps can be used to release a new version for
+`SingleCellExperiment`:
+
+1. Make sure all unit tests are successful.
+2. Tag the current commit on the main branch with a release tag, e.g., `v1.2.3`.
+3. Push the new tag to the upstream [repository],
+   e.g., `git push upstream v1.2.3`
+4. Clean up the `dist` and `build` folders with `tox -e clean`
+   (or `rm -rf dist build`)
+   to avoid confusion with old builds and Sphinx docs.
+5. Run `tox -e build` and check that the files in `dist` have
+   the correct version (no `.dirty` or [git] hash) according to the [git] tag.
+   Also check the sizes of the distributions, if they are too big (e.g., >
+   500KB), unwanted clutter may have been accidentally included.
+6. Run `tox -e publish -- --repository pypi` and check that everything was
+   uploaded to [PyPI] correctly.
+
+[^contrib1]: Even though, these resources focus on open source projects and
+    communities, the general ideas behind collaborating with other developers
+    to collectively create software are general and can be applied to all sorts
+    of environments, including private companies and proprietary code bases.
+
+
+[black]: https://pypi.org/project/black/
+[commonmark]: https://commonmark.org/
+[contribution-guide.org]: http://www.contribution-guide.org/
+[creating a pr]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request
+[descriptive commit message]: https://chris.beams.io/posts/git-commit
+[docstrings]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+[first-contributions tutorial]: https://github.com/firstcontributions/first-contributions
+[flake8]: https://flake8.pycqa.org/en/stable/
+[git]: https://git-scm.com
+[github web interface]: https://docs.github.com/en/github/managing-files-in-a-repository/managing-files-on-github/editing-files-in-your-repository
+[github's code editor]: https://docs.github.com/en/github/managing-files-in-a-repository/managing-files-on-github/editing-files-in-your-repository
+[github's fork and pull request workflow]: https://guides.github.com/activities/forking/
+[guide created by freecodecamp]: https://github.com/freecodecamp/how-to-contribute-to-open-source
+[miniconda]: https://docs.conda.io/en/latest/miniconda.html
+[myst]: https://myst-parser.readthedocs.io/en/latest/syntax/syntax.html
+[other kinds of contributions]: https://opensource.guide/how-to-contribute
+[pre-commit]: https://pre-commit.com/
+[pypi]: https://pypi.org/
+[pyscaffold's contributor's guide]: https://pyscaffold.org/en/stable/contributing.html
+[pytest can drop you]: https://docs.pytest.org/en/stable/usage.html#dropping-to-pdb-python-debugger-at-the-start-of-a-test
+[python software foundation's code of conduct]: https://www.python.org/psf/conduct/
+[restructuredtext]: https://www.sphinx-doc.org/en/master/usage/restructuredtext/
+[sphinx]: https://www.sphinx-doc.org/en/master/
+[tox]: https://tox.readthedocs.io/en/stable/
+[virtual environment]: https://realpython.com/python-virtual-environments-a-primer/
+[virtualenv]: https://virtualenv.pypa.io/en/stable/
+
+
+```{todo} Please review and change the following definitions:
+```
+
+[repository]: https://github.com/<USERNAME>/SingleCellExperiment
+[issue tracker]: https://github.com/<USERNAME>/SingleCellExperiment/issues

{SingleCellExperiment-0.2.5/src/SingleCellExperiment.egg-info → SingleCellExperiment-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.2.5
+Version: 0.3.0
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche
@@ -34,7 +34,7 @@ Readers are available to read AnnData, H5AD or 10x (MTX, H5) V3 formats as `Sing
 ```python
 import singlecellexperiment
 
-sce = singlecellexperiment.readH5AD("tests/data/adata.h5ad")
+sce = singlecellexperiment.read_h5ad("tests/data/adata.h5ad")
 ```
 
 ***OR construct one from scratch***
@@ -43,16 +43,16 @@ sce = singlecellexperiment.readH5AD("tests/data/adata.h5ad")
 from singlecellexperiment import SingleCellExperiment
 
 tse = SingleCellExperiment(
-    assays={"counts": counts}, rowData=df_gr, colData=colData,
-    reducedDims={"tsne": ..., "umap": ...}, altExps={"atac": ...}
+    assays={"counts": counts}, row_data=df_gr, col_data=col_data,
+    reduced_dims={"tsne": ..., "umap": ...}, alternative_experiments={"atac": ...}
 )
 ```
 
-`SingleCellExperiment` extends `SummarizedExperiment`, so most methods from there are applicable here. checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/).
+Since `SingleCellExperiment` extends `SummarizedExperiment`, most methods especially slicing and accessors are applicable here. Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
 
 <!-- pyscaffold-notes -->
 
 ## Note
 
-This project has been set up using PyScaffold 4.1.1. For details and usage
+This project has been set up using PyScaffold 4.5. For details and usage
 information on PyScaffold see https://pyscaffold.org/.

{SingleCellExperiment-0.2.5 → SingleCellExperiment-0.3.0}/README.md

@@ -18,7 +18,7 @@ Readers are available to read AnnData, H5AD or 10x (MTX, H5) V3 formats as `Sing
 ```python
 import singlecellexperiment
 
-sce = singlecellexperiment.readH5AD("tests/data/adata.h5ad")
+sce = singlecellexperiment.read_h5ad("tests/data/adata.h5ad")
 ```
 
 ***OR construct one from scratch***
@@ -27,16 +27,16 @@ sce = singlecellexperiment.readH5AD("tests/data/adata.h5ad")
 from singlecellexperiment import SingleCellExperiment
 
 tse = SingleCellExperiment(
-    assays={"counts": counts}, rowData=df_gr, colData=colData,
-    reducedDims={"tsne": ..., "umap": ...}, altExps={"atac": ...}
+    assays={"counts": counts}, row_data=df_gr, col_data=col_data,
+    reduced_dims={"tsne": ..., "umap": ...}, alternative_experiments={"atac": ...}
 )
 ```
 
-`SingleCellExperiment` extends `SummarizedExperiment`, so most methods from there are applicable here. checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/).
+Since `SingleCellExperiment` extends `SummarizedExperiment`, most methods especially slicing and accessors are applicable here. Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
 
 <!-- pyscaffold-notes -->
 
 ## Note
 
-This project has been set up using PyScaffold 4.1.1. For details and usage
+This project has been set up using PyScaffold 4.5. For details and usage
 information on PyScaffold see https://pyscaffold.org/.

{SingleCellExperiment-0.2.5 → SingleCellExperiment-0.3.0}/docs/conf.py

@@ -78,25 +78,22 @@ extensions = [
 templates_path = ["_templates"]
 
 
-# Configure AutoStructify
-# https://recommonmark.readthedocs.io/en/latest/auto_structify.html
-def setup(app):
-    from recommonmark.transform import AutoStructify
-
-    params = {
-        "enable_auto_toc_tree": True,
-        "auto_toc_tree_section": "Contents",
-        "auto_toc_maxdepth": 2,
-        "enable_eval_rst": True,
-        "enable_math": True,
-        "enable_inline_math": True,
-    }
-    app.add_config_value("recommonmark_config", params, True)
-    app.add_transform(AutoStructify)
-
-
 # Enable markdown
-extensions.append("recommonmark")
+extensions.append("myst_parser")
+
+# Configure MyST-Parser
+myst_enable_extensions = [
+    "amsmath",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "html_image",
+    "linkify",
+    "replacements",
+    "smartquotes",
+    "substitution",
+    "tasklist",
+]
 
 # The suffix of source filenames.
 source_suffix = [".rst", ".md"]
@@ -109,7 +106,7 @@ master_doc = "index"
 
 # General information about the project.
 project = "SingleCellExperiment"
-copyright = "2022, jkanche"
+copyright = "2023, jkanche"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -169,6 +166,14 @@ pygments_style = "sphinx"
 # If this is True, todo emits a warning for each TODO entries. The default is False.
 todo_emit_warnings = True
 
+autodoc_default_options = {
+    'special-members': True,
+    'undoc-members': False,
+    'exclude-members': '__weakref__, __dict__, __str__, __module__, __init__'
+}
+
+autosummary_generate = True
+autosummary_imported_members = True
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -300,8 +305,11 @@ intersphinx_mapping = {
     "sklearn": ("https://scikit-learn.org/stable", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
-    "setuptools": ("https://setuptools.readthedocs.io/en/stable/", None),
+    "setuptools": ("https://setuptools.pypa.io/en/stable/", None),
     "pyscaffold": ("https://pyscaffold.org/en/stable", None),
+    "biocframe": ("https://biocpy.github.io/BiocFrame", None),
+    "genomicranges": ("https://biocpy.github.io/GenomicRanges", None),
+    "singlecellexperiment": ("https://biocpy.github.io/SingleCellExperiment", None),
 }
 
 print(f"loading configurations for {project} {version} ...", file=sys.stderr)

SingleCellExperiment-0.3.0/docs/contributing.md

@@ -0,0 +1,4 @@
+```{include} ../CONTRIBUTING.md
+:relative-docs: docs/
+:relative-images:
+```

{SingleCellExperiment-0.2.5 → SingleCellExperiment-0.3.0}/docs/index.md

@@ -12,24 +12,26 @@ pip install singlecellexperiment
 ```
 ## Contents
 
-* [Overview](readme)
-* [Tutorial](tutorial)
-* [License](license)
-* [Authors](authors)
-* [Changelog](changelog)
-* [Module Reference](api/modules)
+```{toctree}
+:maxdepth: 2
+
+Overview <readme>
+Tutorial <tutorial>
+Module Reference <api/modules>
+Contributions & Help <contributing>
+License <license>
+Authors <authors>
+Changelog <changelog>
+```
 
 
 ## Indices and tables
 
-```eval_rst
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-```
+- {ref}`genindex`
+- {ref}`modindex`
+- {ref}`search`
 
 [Sphinx]: http://www.sphinx-doc.org/
 [Markdown]: https://daringfireball.net/projects/markdown/
 [reStructuredText]: http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
-[recommonmark]: https://recommonmark.readthedocs.io/en/latest
-[autostructify]: https://recommonmark.readthedocs.io/en/latest/auto_structify.html
+[MyST]: https://myst-parser.readthedocs.io/en/latest/

SingleCellExperiment-0.3.0/docs/license.md

@@ -0,0 +1,5 @@
+# License
+
+```{literalinclude} ../LICENSE.txt
+:language: text
+```

{SingleCellExperiment-0.2.5 → SingleCellExperiment-0.3.0}/docs/readme.md

@@ -18,7 +18,7 @@ Readers are available to read AnnData, H5AD or 10x (MTX, H5) V3 formats as `Sing
 ```python
 import singlecellexperiment
 
-sce = singlecellexperiment.readH5AD("tests/data/adata.h5ad")
+sce = singlecellexperiment.read_h5ad("tests/data/adata.h5ad")
 ```
 
 ***OR construct one from scratch***
@@ -27,16 +27,16 @@ sce = singlecellexperiment.readH5AD("tests/data/adata.h5ad")
 from singlecellexperiment import SingleCellExperiment
 
 tse = SingleCellExperiment(
-    assays={"counts": counts}, rowData=df_gr, colData=colData,
-    reducedDims={"tsne": ..., "umap": ...}, altExps={"atac": ...}
+    assays={"counts": counts}, row_data=df_gr, col_data=col_data,
+    reduced_dims={"tsne": ..., "umap": ...}, alternative_experiments={"atac": ...}
 )
 ```
 
-`SingleCellExperiment` extends `SummarizedExperiment`, so most methods from there are applicable here. checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/).
+Since `SingleCellExperiment` extends `SummarizedExperiment`, most methods especially slicing and accessors are applicable here. Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
 
 <!-- pyscaffold-notes -->
 
 ## Note
 
-This project has been set up using PyScaffold 4.1.1. For details and usage
+This project has been set up using PyScaffold 4.5. For details and usage
 information on PyScaffold see https://pyscaffold.org/.

{SingleCellExperiment-0.2.5 → SingleCellExperiment-0.3.0}/docs/requirements.txt

@@ -2,7 +2,6 @@
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
-recommonmark
+myst-parser[linkify]
 sphinx>=3.2.1
-sphinx-rtd-theme
 furo