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Update instance repo from cookiecutter template
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@@ -46,6 +46,8 @@ rst-roles = | |
| class, | ||
| func, | ||
| ref, | ||
| cite:p, | ||
| cite:t, | ||
| rst-directives = | ||
| envvar, | ||
| exception, | ||
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| @@ -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 | ||
|
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| - 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 |
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| @@ -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. |
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| Original file line number | Diff line number | Diff line change |
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| @@ -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 |
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| @@ -0,0 +1,65 @@ | ||
| {{ fullname | escape | underline}} | ||
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| .. currentmodule:: {{ module }} | ||
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| .. add toctree option to make autodoc generate the pages | ||
| .. autoclass:: {{ objname }} | ||
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| {% block attributes %} | ||
| {% if attributes %} | ||
| Attributes table | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
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| .. autosummary:: | ||
| {% for item in attributes %} | ||
| ~{{ fullname }}.{{ item }} | ||
| {%- endfor %} | ||
| {% endif %} | ||
| {% endblock %} | ||
|
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| {% block methods %} | ||
| {% if methods %} | ||
| Methods table | ||
| ~~~~~~~~~~~~~ | ||
|
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| .. autosummary:: | ||
| {% for item in methods %} | ||
| {%- if item != '__init__' %} | ||
| ~{{ fullname }}.{{ item }} | ||
| {%- endif -%} | ||
| {%- endfor %} | ||
| {% endif %} | ||
| {% endblock %} | ||
|
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| {% block attributes_documentation %} | ||
| {% if attributes %} | ||
| Attributes | ||
| ~~~~~~~~~~~ | ||
|
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| {% for item in attributes %} | ||
| {{ item }} | ||
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ||
|
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| .. autoattribute:: {{ [objname, item] | join(".") }} | ||
| {%- endfor %} | ||
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| {% endif %} | ||
| {% endblock %} | ||
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| {% block methods_documentation %} | ||
| {% if methods %} | ||
| Methods | ||
| ~~~~~~~ | ||
|
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| {% for item in methods %} | ||
| {%- if item != '__init__' %} | ||
| {{ item }} | ||
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ||
|
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| .. automethod:: {{ [objname, item] | join(".") }} | ||
| {%- endif -%} | ||
| {%- endfor %} | ||
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| {% endif %} | ||
| {% endblock %} |
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@@ -34,4 +34,5 @@ | |
| :toctree: generated | ||
| pl.basic_plot | ||
| pl.BasicClass | ||
| ``` | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,29 @@ | ||
| # code from https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py | ||
| # with some minor adjustment | ||
| import re | ||
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| from sphinx.application import Sphinx | ||
| from sphinx.ext.napoleon import NumpyDocstring | ||
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| 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 | ||
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| 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 | ||
|
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| def setup(app: Sphinx): | ||
| """Set app.""" | ||
| NumpyDocstring._parse_returns_section = _parse_returns_section |
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