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Automated template update from cookiecutter-scverse (#61)
* Update sync.yaml * Automated template update from cookiecutter-scverse * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix merge conflicts * Fix merge conflict Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: grst <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gregor Sturm <[email protected]>
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‎.cruft.json

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{
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"template": "https://github.com/scverse/cookiecutter-scverse",
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"commit": "8148f720e622a82345bfc18b74b2bd288d12f7d5",
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"commit": "28f47a97470826ca5000df24fd272e0d32d1c6fa",
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"context": {
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"cookiecutter": {
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"project_name": "infercnvpy",
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"github_user": "grst",
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"project_repo": "https://github.com/icbi-lab/infercnvpy",
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"license": "BSD 3-Clause License",
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"_copy_without_render": [".github/workflows/**.yaml"],
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"_copy_without_render": [
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".github/workflows/**.yaml",
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"docs/_templates/autosummary/**.rst"
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],
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"_template": "https://github.com/scverse/cookiecutter-scverse"
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}
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},
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"directory": null,
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"checkout": "v0.0.2"
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"checkout": "v0.0.3"
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}

‎.flake8

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# whitespace before : -> black does not adhere to PEP8
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# line break before binary operator -> black does not adhere to PEP8
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# missing whitespace after ,', ';', or ':' -> black does not adhere to PEP8
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# continuation line over-indented for hanging indent -> black does not adhere to PEP8
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# E266 too many leading '#' for block comment -> this is fine for indicating sections
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# too many leading '#' for block comment -> this is fine for indicating sections
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# Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
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# allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
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# allow I, O, l as variable names -> I is the identity matrix
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# Missing docstring in public package
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# ... imported but unused
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# Missing docstring in public module
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# Missing docstring in __init__
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# Do not perform function calls in argument defaults.
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# Errors from function calls in argument defaults. These are fine when the result is immutable.
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# line break before binary operator
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# Missing docstring in magic method
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# whitespace before ':'
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# format string does contain unindexed parameters
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# first line should end with a period [Bug: doesn't work with single-line docstrings]
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class,
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func,
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ref,
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cite:p,
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cite:t,
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rst-directives =
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envvar,
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exception,

‎.github/ISSUE_TEMPLATE/bug_report.yml

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name: Bug report
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description: Report something that is broken or incorrect
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labels: bug
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body:
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- type: markdown
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attributes:
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value: |
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**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
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detailing how to provide the necessary information for us to reproduce your bug. In brief:
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* Please provide exact steps how to reproduce the bug in a clean Python environment.
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* In case it's not clear what's causing this bug, please provide the data or the data generation procecure.
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* Sometimes it is not possible to share the data but usually it is possible to replicate problems on publicly
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available datasets or to share a subset of your data.
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- type: textarea
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id: report
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attributes:
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label: Report
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description: A clear and concise description of what the bug is.
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validations:
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required: true
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- type: textarea
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id: versions
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attributes:
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label: Version information
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description: |
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Please paste below the output of
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```python
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import session_info
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session_info.show(html=False, dependencies=True)
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```
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placeholder: |
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-----
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anndata 0.8.0rc2.dev27+ge524389
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session_info 1.0.0
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-----
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asttokens NA
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awkward 1.8.0
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backcall 0.2.0
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cython_runtime NA
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dateutil 2.8.2
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debugpy 1.6.0
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decorator 5.1.1
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entrypoints 0.4
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executing 0.8.3
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h5py 3.7.0
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ipykernel 6.15.0
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jedi 0.18.1
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mpl_toolkits NA
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natsort 8.1.0
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numpy 1.22.4
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packaging 21.3
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pandas 1.4.2
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parso 0.8.3
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pexpect 4.8.0
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pickleshare 0.7.5
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pkg_resources NA
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prompt_toolkit 3.0.29
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psutil 5.9.1
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ptyprocess 0.7.0
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pure_eval 0.2.2
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pydev_ipython NA
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pydevconsole NA
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pydevd 2.8.0
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pydevd_file_utils NA
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pydevd_plugins NA
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pydevd_tracing NA
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pygments 2.12.0
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pytz 2022.1
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scipy 1.8.1
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setuptools 62.5.0
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setuptools_scm NA
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six 1.16.0
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stack_data 0.3.0
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tornado 6.1
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traitlets 5.3.0
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wcwidth 0.2.5
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zmq 23.1.0
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-----
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IPython 8.4.0
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jupyter_client 7.3.4
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jupyter_core 4.10.0
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-----
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Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
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Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
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-----
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Session information updated at 2022-07-07 17:55

‎.github/ISSUE_TEMPLATE/config.yml

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blank_issues_enabled: false
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contact_links:
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- name: Scverse Community Forum
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url: https://discourse.scverse.org/
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about: If you have questions about “How to do X”, please ask them here.

‎.github/ISSUE_TEMPLATE/feature_request.yml

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name: Feature request
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description: Propose a new feature for infercnvpy
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labels: enhancement
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body:
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- type: textarea
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id: description
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attributes:
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label: Description of feature
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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.
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validations:
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required: true

‎.readthedocs.yaml

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python: "3.10"
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sphinx:
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configuration: docs/conf.py
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# disable this for more lenient docs builds
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fail_on_warning: true
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python:
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install:

‎README.md

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## Installation
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You need to have Python 3.8 or newer installed on your system. If you don't have
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Python installed, we recommend installing [Miniconda](https://docs.conda.io/en/latest/miniconda.html).
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Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
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There are several alternative options to install infercnvpy:
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‎docs/_templates/autosummary/class.rst

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{{ fullname | escape | underline}}
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.. currentmodule:: {{ module }}
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.. add toctree option to make autodoc generate the pages
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.. autoclass:: {{ objname }}
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{% block attributes %}
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{% if attributes %}
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Attributes table
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~~~~~~~~~~~~~~~~~~
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.. autosummary::
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{% for item in attributes %}
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~{{ fullname }}.{{ item }}
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{%- endfor %}
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{% endif %}
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{% endblock %}
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{% block methods %}
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{% if methods %}
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Methods table
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~~~~~~~~~~~~~
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.. autosummary::
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{% for item in methods %}
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{%- if item != '__init__' %}
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~{{ fullname }}.{{ item }}
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{%- endif -%}
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{%- endfor %}
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{% endif %}
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{% endblock %}
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{% block attributes_documentation %}
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{% if attributes %}
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Attributes
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~~~~~~~~~~~
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{% for item in attributes %}
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{{ item }}
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. autoattribute:: {{ [objname, item] | join(".") }}
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{%- endfor %}
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{% endif %}
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{% endblock %}
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{% block methods_documentation %}
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{% if methods %}
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Methods
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~~~~~~~
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{% for item in methods %}
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{%- if item != '__init__' %}
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{{ item }}
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automethod:: {{ [objname, item] | join(".") }}
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{%- endif -%}
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{%- endfor %}
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{% endif %}
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{% endblock %}

‎docs/conf.py

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# -- Project information -----------------------------------------------------
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info = metadata("infercnvpy")
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project = info["Name"]
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project_name = info["Name"]
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author = info["Author"]
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copyright = f"{datetime.now():%Y}, {author}."
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version = info["Version"]
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repository_url = "https://github.com/" + "grst" + "/" + project_name
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# The full version, including alpha/beta/rc tags
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release = info["Version"]
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html_context = {
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"display_github": True, # Integrate GitHub
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"github_user": "icbi-lab", # Username
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"github_repo": project, # Repo name
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"github_repo": project_name, # Repo name
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"github_version": "main", # Version
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"conf_py_path": "/docs/", # Path in the checkout to the docs root
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}
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# Add any Sphinx extension module names here, as strings.
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# They can be extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
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extensions = [
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"myst_parser",
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"myst_nb",
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"sphinx_copybutton",
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"sphinx.ext.autodoc",
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"sphinx.ext.intersphinx",
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"sphinx.ext.autosummary",
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"sphinx.ext.napoleon",
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"sphinxcontrib.bibtex",
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"sphinx_autodoc_typehints",
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"scanpydoc.definition_list_typed_field",
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"nbsphinx",
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"sphinx.ext.mathjax",
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*[p.stem for p in (HERE / "extensions").glob("*.py")],
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]
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napoleon_use_rtype = True # having a separate entry generally helps readability
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napoleon_use_param = True
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myst_heading_anchors = 3 # create anchors for h1-h3
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myst_enable_extensions = [
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"amsmath",
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"colon_fence",
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"deflist",
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"dollarmath",
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"html_image",
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"html_admonition",
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]
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myst_url_schemes = ("http", "https", "mailto")
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nb_output_stderr = "remove"
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nb_execution_mode = "off"
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nb_merge_streams = True
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typehints_defaults = "braces"
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source_suffix = {
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".rst": "restructuredtext",
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".ipynb": "myst-nb",
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".myst": "myst-nb",
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}
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intersphinx_mapping = {
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"scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
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# The theme to use for HTML and HTML Help pages. See the documentation for
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html_theme = "furo"
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html_theme = "sphinx_book_theme"
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html_static_path = ["_static"]
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html_title = project_name
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html_theme_options = {
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"repository_url": repository_url,
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"use_repository_button": True,
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}
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pygments_style = "sphinx"
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pygments_style = "default"
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nitpick_ignore = [
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# If building the documentation fails because of a missing link that is outside your control,

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