scverse · scverse-bot · Oct 19, 2022 · Oct 19, 2022 · Oct 19, 2022
diff --git a/.flake8 b/.flake8
@@ -46,6 +46,8 @@ rst-roles =
     class,
     func,
     ref,
+    cite:p,
+    cite:t,
 rst-directives =
     envvar,
     exception,

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -0,0 +1,89 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+    - type: markdown
+      attributes:
+          value: |
+              **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+              detailing how to provide the necessary information for us to reproduce your bug. In brief:
+                * Please provide exact steps how to reproduce the bug in a clean Python environment.
+                * In case it's not clear what's causing this bug, please provide the data or the data generation procecure.
+                * Sometimes it is not possible to share the data but usually it is possible to replicate problems on publicly
+                  available datasets or to share a subset of your data.
+
+    - type: textarea
+      id: report
+      attributes:
+          label: Report
+          description: A clear and concise description of what the bug is.
+      validations:
+          required: true
+
+    - type: textarea
+      id: versions
+      attributes:
+          label: Version information
+          description: |
+              Please paste below the output of
+
+              ```python
+              import session_info
+              session_info.show(html=False, dependencies=True)
+              ```
+          placeholder: |
+              -----
+              anndata             0.8.0rc2.dev27+ge524389
+              session_info        1.0.0
+              -----
+              asttokens           NA
+              awkward             1.8.0
+              backcall            0.2.0
+              cython_runtime      NA
+              dateutil            2.8.2
+              debugpy             1.6.0
+              decorator           5.1.1
+              entrypoints         0.4
+              executing           0.8.3
+              h5py                3.7.0
+              ipykernel           6.15.0
+              jedi                0.18.1
+              mpl_toolkits        NA
+              natsort             8.1.0
+              numpy               1.22.4
+              packaging           21.3
+              pandas              1.4.2
+              parso               0.8.3
+              pexpect             4.8.0
+              pickleshare         0.7.5
+              pkg_resources       NA
+              prompt_toolkit      3.0.29
+              psutil              5.9.1
+              ptyprocess          0.7.0
+              pure_eval           0.2.2
+              pydev_ipython       NA
+              pydevconsole        NA
+              pydevd              2.8.0
+              pydevd_file_utils   NA
+              pydevd_plugins      NA
+              pydevd_tracing      NA
+              pygments            2.12.0
+              pytz                2022.1
+              scipy               1.8.1
+              setuptools          62.5.0
+              setuptools_scm      NA
+              six                 1.16.0
+              stack_data          0.3.0
+              tornado             6.1
+              traitlets           5.3.0
+              wcwidth             0.2.5
+              zmq                 23.1.0
+              -----
+              IPython             8.4.0
+              jupyter_client      7.3.4
+              jupyter_core        4.10.0
+              -----
+              Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
+              Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
+              -----
+              Session information updated at 2022-07-07 17:55
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+    - name: Scverse Community Forum
+      url: https://discourse.scverse.org/
+      about: If you have questions about “How to do X”, please ask them here.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for cookiecutter-scverse-instance
+labels: enhancement
+body:
+    - type: textarea
+      id: description
+      attributes:
+          label: Description of feature
+          description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+      validations:
+          required: true
diff --git a/.github/workflows/sync.yaml b/.github/workflows/sync.yaml
@@ -0,0 +1,46 @@
+name: Sync Template
+
+on:
+    workflow_dispatch:
+    schedule:
+        - cron: "0 2 * * *" # every night at 2:00 UTC
+
+jobs:
+    sync:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.10"
+            - name: Install dependencies
+              # for now, pin cookiecutter version, due to https://github.com/cruft/cruft/issues/166
+              run: python -m pip install --upgrade cruft "cookiecutter<2" pre-commit toml
+            - name: Find Latest Tag
+              uses: oprypin/find-latest-tag@v1.1.0
+              id: get-latest-tag
+              with:
+                  repository: scverse/cookiecutter-scverse
+                  releases-only: false
+                  sort-tags: true
+                  regex: '^v\d+\.\d+\.\d+$' # vX.X.X
+            - name: Sync
+              run: |
+                  cruft update --checkout ${{ steps.get-latest-tag.outputs.tag }} --skip-apply-ask --project-dir .
+            - name: Create Pull Request
+              uses: peter-evans/create-pull-request@v4
+              with:
+                  commit-message: Automated template update from cookiecutter-scverse
+                  branch: template-update
+                  title: Automated template update from cookiecutter-scverse
+                  body: |
+                      A new version of the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse/releases)
+                      got released. This PR adds all new changes to your repository and helps to to stay in sync with
+                      the latest best-practice template maintained by the scverse team.
+
+                      **If a merge conflict arised, a `.rej` file with the rejected patch is generated. You'll need to
+                      manually merge these changes.**
+
+                      For more information about the template sync, please refer to the
+                      [template documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#automated-template-sync).
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0-alpha.1
+      rev: v3.0.0-alpha.2
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
@@ -44,7 +44,7 @@ repos:
           - id: trailing-whitespace
           - id: check-case-conflict
     - repo: https://github.com/myint/autoflake
-      rev: v1.7.1
+      rev: v1.7.6
       hooks:
           - id: autoflake
             args:
@@ -64,7 +64,16 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.0.0
+      rev: v3.1.0
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py38-plus, --keep-runtime-typing]
+    - repo: local
+      hooks:
+          - id: forbid-to-commit
+            name: Don't commit rej files
+            entry: |
+                Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+                Fix the merge conflicts manually and remove the .rej files.
+            language: fail
+            files: '.*\.rej$'
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -6,6 +6,7 @@ build:
         python: "3.10"
 sphinx:
     configuration: docs/conf.py
+    # disable this for more lenient docs builds
     fail_on_warning: true
 python:
     install:

diff --git a/README.md b/README.md
@@ -18,7 +18,7 @@ Please refer to the [documentation][link-docs]. In particular, the
 ## Installation
 
 You need to have Python 3.8 or newer installed on your system. If you don't have
-Python installed, we recommend installing [Miniconda](https://docs.conda.io/en/latest/miniconda.html).
+Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
 
 There are several alternative options to install cookiecutter-scverse-instance:
 

diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
@@ -0,0 +1,65 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. add toctree option to make autodoc generate the pages
+
+.. autoclass:: {{ objname }}
+
+{% block attributes %}
+{% if attributes %}
+Attributes table
+~~~~~~~~~~~~~~~~~~
+
+.. autosummary::
+{% for item in attributes %}
+    ~{{ fullname }}.{{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
+
+{% block methods %}
+{% if methods %}
+Methods table
+~~~~~~~~~~~~~
+
+.. autosummary::
+{% for item in methods %}
+    {%- if item != '__init__' %}
+    ~{{ fullname }}.{{ item }}
+    {%- endif -%}
+{%- endfor %}
+{% endif %}
+{% endblock %}
+
+{% block attributes_documentation %}
+{% if attributes %}
+Attributes
+~~~~~~~~~~~
+
+{% for item in attributes %}
+{{ item }}
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. autoattribute:: {{ [objname, item] | join(".") }}
+{%- endfor %}
+
+{% endif %}
+{% endblock %}
+
+{% block methods_documentation %}
+{% if methods %}
+Methods
+~~~~~~~
+
+{% for item in methods %}
+{%- if item != '__init__' %}
+{{ item }}
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automethod:: {{ [objname, item] | join(".") }}
+{%- endif -%}
+{%- endfor %}
+
+{% endif %}
+{% endblock %}
diff --git a/docs/api.md b/docs/api.md
@@ -34,4 +34,5 @@
     :toctree: generated
 
     pl.basic_plot
+    pl.BasicClass
 ```
diff --git a/docs/conf.py b/docs/conf.py
@@ -17,10 +17,11 @@
 # -- Project information -----------------------------------------------------
 
 info = metadata("cookiecutter-scverse-instance")
-project = info["Name"]
+project_name = info["Name"]
 author = info["Author"]
 copyright = f"{datetime.now():%Y}, {author}."
 version = info["Version"]
+repository_url = "https://github.com/" + "scverse" + "/" + project_name
 
 # The full version, including alpha/beta/rc tags
 release = info["Version"]
@@ -33,7 +34,7 @@
 html_context = {
     "display_github": True,  # Integrate GitHub
     "github_user": "scverse",  # Username
-    "github_repo": project,  # Repo name
+    "github_repo": project_name,  # Repo name
     "github_version": "main",  # Version
     "conf_py_path": "/docs/",  # Path in the checkout to the docs root
 }
@@ -43,15 +44,14 @@
 # Add any Sphinx extension module names here, as strings.
 # They can be extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
-    "myst_parser",
+    "myst_nb",
+    "sphinx_copybutton",
     "sphinx.ext.autodoc",
     "sphinx.ext.intersphinx",
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
     "sphinxcontrib.bibtex",
     "sphinx_autodoc_typehints",
-    "scanpydoc.definition_list_typed_field",
-    "nbsphinx",
     "sphinx.ext.mathjax",
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
 ]
@@ -65,13 +65,31 @@
 napoleon_use_rtype = True  # having a separate entry generally helps readability
 napoleon_use_param = True
 myst_heading_anchors = 3  # create anchors for h1-h3
+myst_enable_extensions = [
+    "amsmath",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "html_image",
+    "html_admonition",
+]
+myst_url_schemes = ("http", "https", "mailto")
+nb_output_stderr = "remove"
+nb_execution_mode = "off"
+nb_merge_streams = True
+typehints_defaults = "braces"
+
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".ipynb": "myst-nb",
+    ".myst": "myst-nb",
+}
 
 intersphinx_mapping = {
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
 }
 
-nbsphinx_execute = "never"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -84,10 +102,16 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "furo"
+html_theme = "sphinx_book_theme"
 html_static_path = ["_static"]
+html_title = project_name
+
+html_theme_options = {
+    "repository_url": repository_url,
+    "use_repository_button": True,
+}
 
-pygments_style = "sphinx"
+pygments_style = "default"
 
 nitpick_ignore = [
     # If building the documentation fails because of a missing link that is outside your control,