diff --git a/.cruft.json b/.cruft.json
index f2f3b97..e13da47 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,6 +1,6 @@
 {
     "template": "https://github.com/scverse/cookiecutter-scverse",
-    "commit": "8148f720e622a82345bfc18b74b2bd288d12f7d5",
+    "commit": "28f47a97470826ca5000df24fd272e0d32d1c6fa",
     "context": {
         "cookiecutter": {
             "project_name": "infercnvpy",
@@ -11,10 +11,13 @@
             "github_user": "grst",
             "project_repo": "https://github.com/icbi-lab/infercnvpy",
             "license": "BSD 3-Clause License",
-            "_copy_without_render": [".github/workflows/**.yaml"],
+            "_copy_without_render": [
+                ".github/workflows/**.yaml",
+                "docs/_templates/autosummary/**.rst"
+            ],
             "_template": "https://github.com/scverse/cookiecutter-scverse"
         }
     },
     "directory": null,
-    "checkout": "v0.0.2"
+    "checkout": "v0.0.3"
 }
diff --git a/.flake8 b/.flake8
index 8d014c6..5535753 100644
--- a/.flake8
+++ b/.flake8
@@ -10,32 +10,28 @@ ignore =
     E501
     # whitespace before : -> black does not adhere to PEP8
     E203
+    # line break before binary operator -> black does not adhere to PEP8
+    W503
     # missing whitespace after ,', ';', or ':' -> black does not adhere to PEP8
     E231
     # continuation line over-indented for hanging indent -> black does not adhere to PEP8
     E126
-    # E266 too many leading '#' for block comment -> this is fine for indicating sections
+    # too many leading '#' for block comment -> this is fine for indicating sections
     E262
     # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
     E731
-    # allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
+    # allow I, O, l as variable names -> I is the identity matrix
     E741
     # Missing docstring in public package
     D104
-    # ... imported but unused
-    F401
     # Missing docstring in public module
     D100
     # Missing docstring in __init__
     D107
-    # Do not perform function calls in argument defaults.
+    # Errors from function calls in argument defaults. These are fine when the result is immutable.
     B008
-    # line break before binary operator
-    W503
     # Missing docstring in magic method
     D105
-    # whitespace before ':'
-    E203
     # format string does contain unindexed parameters
     P101
     # first line should end with a period [Bug: doesn't work with single-line docstrings]
@@ -58,6 +54,8 @@ 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
new file mode 100644
index 0000000..9dfd4ac
--- /dev/null
+++ 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
new file mode 100644
index 0000000..5cad625
--- /dev/null
+++ 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
new file mode 100644
index 0000000..26123f3
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for infercnvpy
+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/.readthedocs.yaml b/.readthedocs.yaml
index 170325e..9e5d5fa 100644
--- 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
index dbacf35..3f6776e 100644
--- a/README.md
+++ b/README.md
@@ -33,7 +33,7 @@ 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 infercnvpy:
 
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
new file mode 100644
index 0000000..49f45ed
--- /dev/null
+++ 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/conf.py b/docs/conf.py
index 2dcaf96..a693321 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -17,10 +17,11 @@
 # -- Project information -----------------------------------------------------
 
 info = metadata("infercnvpy")
-project = info["Name"]
+project_name = info["Name"]
 author = info["Author"]
 copyright = f"{datetime.now():%Y}, {author}."
 version = info["Version"]
+repository_url = "https://github.com/" + "grst" + "/" + 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": "icbi-lab",  # 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")],
 ]
@@ -65,6 +65,25 @@
 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 = {
     "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
@@ -95,10 +114,16 @@
 # 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,
diff --git a/docs/developer_docs.md b/docs/developer_docs.md
index 3854bd5..4d1c9f1 100644
--- a/docs/developer_docs.md
+++ b/docs/developer_docs.md
@@ -20,6 +20,7 @@ On the RTD dashboard choose "Import a Project" and follow the instructions to ad
     that break the documentation. To do so, got to `Admin -> Advanced Settings`, check the
     `Build pull requests for this projects` option, and click `Save`. For more information, please refer to
     the [official RTD documentation](https://docs.readthedocs.io/en/stable/pull-requests.html).
+-   If you find the RTD builds are failing, you can disable the `fail_on_warning` option in `.readthedocs.yaml`.
 
 ### Coverage tests with _Codecov_
 
@@ -92,6 +93,8 @@ The following pre-commit checks are for errors and inconsistencies:
     -   **check-case-conflict**: check files that would conflict with case-insensitive file systems.
 -   [pyupgrade](https://github.com/asottile/pyupgrade):
     upgrade syntax for newer versions of the language.
+-   **forbid-to-commit**: Make sure that `*.rej` files cannot be commited. These files are created by the
+    [automated template sync](#automated-template-sync) if there's a merge conflict and need to be addressed manually.
 
 #### Notes on pre-commit checks
 
@@ -240,6 +243,32 @@ in the root of the repository. Continuous integration will automatically run the
 
 [scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests
 
+### Automated template sync
+
+Automated template sync is enabled by default. This means that every night, a GitHub action runs [cruft][] to check
+if a new version of the `scverse-cookiecutter` template got released. If there are any new changes, a pull request
+proposing these changes is created automatically. This helps keeping the repository up-to-date with the latest
+coding standards.
+
+It may happen that a template sync results in a merge conflict. If this is the case a `*.ref` file with the
+diff is created. You need to manually address these changes and remove the `.rej` file when you are done.
+The pull request can only be merged after all `*.rej` files have been removed.
+
+:::{tip}
+The following hints may be useful to work with the template sync:
+
+-   GitHub automatically disables scheduled actions if there has been not activity to the repository for 60 days.
+    You can re-enable or manually trigger the sync by navigating to `Actions` -> `Sync Template` in your GitHub repository.
+-   If you want to ignore certain files from the template update, you can add them to the `[tool.cruft]` section in the
+    `pyproject.toml` file in the root of your repository. More details are described in the
+    [cruft documentation][cruft-update-project].
+-   To disable the sync entirely, simply remove the file `.github/workflows/sync.yaml`.
+
+:::
+
+[cruft]: https://cruft.github.io/cruft/
+[cruft-update-project]: https://cruft.github.io/cruft/#updating-a-project
+
 ### Making a release
 
 #### Updating the version number
@@ -289,15 +318,15 @@ Please write documentation for your package. This project uses [sphinx][] with t
 
 -   the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
 -   [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
--   Jupyter notebooks as tutorials through [nbsphinx][] (See [Tutorials with nbsphinx](#tutorials-with-nbsphinx-and-jupyter-notebooks))
+-   Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
 -   [Sphinx autodoc typehints][], to automatically reference annotated input and output types
 
 See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
 on how to write documentation.
 
-### Tutorials with nbsphinx and jupyter notebooks
+### Tutorials with myst-nb and jupyter notebooks
 
-The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [nbsphinx][].
+The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
 Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
 It is your reponsibility to update and re-run the notebook whenever necessary.
 
@@ -305,8 +334,6 @@ If you are interested in automatically running notebooks as part of the continuo
 out [this feature request](https://github.com/scverse/cookiecutter-scverse/issues/40) in the `cookiecutter-scverse`
 repository.
 
-[nbsphinx]: https://github.com/spatialaudio/nbsphinx
-
 #### Hints
 
 -   If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
@@ -329,7 +356,7 @@ open _build/html/index.html
 [codecov docs]: https://docs.codecov.com/docs
 [pre-commit.ci]: https://pre-commit.ci/
 [readthedocs.org]: https://readthedocs.org/
-[nbshpinx]: https://github.com/spatialaudio/nbsphinx
+[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
 [jupytext]: https://jupytext.readthedocs.io/en/latest/
 [pre-commit]: https://pre-commit.com/
 [anndata]: https://github.com/scverse/anndata
diff --git a/docs/extensions/.gitkeep b/docs/extensions/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
new file mode 100644
index 0000000..9447813
--- /dev/null
+++ b/docs/extensions/typed_returns.py
@@ -0,0 +1,29 @@
+# code from https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py
+# with some minor adjustment
+import re
+
+from sphinx.application import Sphinx
+from sphinx.ext.napoleon import NumpyDocstring
+
+
+def _process_return(lines):
+    for line in lines:
+        m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
+        if m:
+            # Once this is in scanpydoc, we can use the fancy hover stuff
+            yield f'-{m["param"]} (:class:`~{m["type"]}`)'
+        else:
+            yield line
+
+
+def _parse_returns_section(self, section):
+    lines_raw = list(_process_return(self._dedent(self._consume_to_next_section())))
+    lines = self._format_block(":returns: ", lines_raw)
+    if lines and lines[-1]:
+        lines.append("")
+    return lines
+
+
+def setup(app: Sphinx):
+    """Set app."""
+    NumpyDocstring._parse_returns_section = _parse_returns_section
diff --git a/pyproject.toml b/pyproject.toml
index 989f683..cf25e77 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,7 +29,9 @@ dependencies = [
     'gtfparse>=1.2.1',
     'pycairo>=1.20; sys_platform == "win32"',
     'leidenalg',
-    'pyreadr'
+    'pyreadr',
+    # for debug logging (referenced from the issue template)
+    "session-info",
 ]
 
 [project.optional-dependencies]
@@ -43,16 +45,15 @@ dev = [
 ]
 doc = [
     "sphinx>=4.2",
-    "furo",
-    "myst-parser",
+    "sphinx-book-theme>=0.3.3",
+    "myst-nb",
     "sphinxcontrib-bibtex>=1.0.0",
-    "scanpydoc[typehints]>=0.7.4",
+    "sphinx-autodoc-typehints",
     # for tutorial
-    'nbsphinx>=0.6.0,!=0.8.8', # https://github.com/spatialaudio/nbsphinx/issues/620, should be patched in >=0.8.9
-    'jupytext',
+    "ipykernel",
+    "sphinx-copybutton",
     'pycairo',
     'jupyter_client',
-    'ipykernel',
 ]
 test = [
     "pytest",
@@ -108,3 +109,15 @@ exclude = '''
 
 [tool.jupytext]
 formats = "ipynb,md"
+
+[tool.cruft]
+skip = [
+    "tests",
+    "src/**/__init__.py",
+    "src/**/basic.py",
+    "docs/api.md",
+    "docs/changelog.md",
+    "docs/references.bib",
+    "docs/references.md",
+    "docs/notebooks/example.ipynb"
+]