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Merge pull request #154 from theislab/development
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update docs and python versions
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AnnaChristina committed Jun 27, 2023
2 parents 1ed3cce + 05fca3f commit 216fd57
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Showing 368 changed files with 8,330 additions and 12,058 deletions.
2 changes: 1 addition & 1 deletion .cookietemple.yml
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Expand Up @@ -15,5 +15,5 @@ full_name: Anna Schaar
email: anna.schaar@helmholtz-muenchen.de
project_name: ncem
project_short_description: ncem. Learning cell communication from spatial graphs of cells.
version: 0.1.4
version: 0.1.5
license: BSD-3-Clause
4 changes: 2 additions & 2 deletions .github/release-drafter.yml
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@@ -1,5 +1,5 @@
name-template: "0.1.4 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
tag-template: 0.1.4 # <<COOKIETEMPLE_FORCE_BUMP>>
name-template: "0.1.5 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
tag-template: 0.1.5 # <<COOKIETEMPLE_FORCE_BUMP>>
categories:
- title: "🚀 Features"
labels:
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4 changes: 2 additions & 2 deletions .github/workflows/build_package.yml
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Expand Up @@ -9,14 +9,14 @@ jobs:
strategy:
matrix:
os: [macos-latest, ubuntu-latest, windows-latest]
python: [3.7, 3.8]
python: [3.8]

steps:
- uses: actions/checkout@v2
name: Check out source-code repository

- name: Setup Python
uses: actions/setup-python@v2
uses: actions/setup-python@v4.3.0
with:
python-version: ${{ matrix.python }}

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2 changes: 1 addition & 1 deletion .github/workflows/main_master_branch_protection.yml
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Expand Up @@ -40,7 +40,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Set up Python
uses: actions/setup-python@v2
uses: actions/setup-python@v4.3.0
with:
python-version: "3.8"
# PRs to the repository master branch are only ok if coming from any patch or release branch
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2 changes: 1 addition & 1 deletion .github/workflows/publish_docs.yml
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Expand Up @@ -11,7 +11,7 @@ jobs:
name: Check out source-code repository

- name: Setup Python
uses: actions/setup-python@v1
uses: actions/setup-python@v4.3.0
with:
python-version: 3.8

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4 changes: 2 additions & 2 deletions .github/workflows/publish_package.yml
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Expand Up @@ -15,7 +15,7 @@ jobs:
fetch-depth: 2

- name: Set up Python
uses: actions/setup-python@v2.1.4
uses: actions/setup-python@v4.3.0
with:
python-version: "3.8"

Expand All @@ -31,7 +31,7 @@ jobs:
- name: Publish package on PyPI
uses: pypa/gh-action-pypi-publish@v1.4.2
with:
# TODO COOKIETEMPLE: Configure your PyPI Token to enable automatic deployment to PyPi on releases
# COOKIETEMPLE: Configure your PyPI Token to enable automatic deployment to PyPi on releases
# https://help.github.com/en/actions/configuring-and-managing-workflows/creating-and-storing-encrypted-secrets
user: __token__
password: ${{ secrets.PYPI_TOKEN }}
2 changes: 1 addition & 1 deletion .github/workflows/run_cookietemple_lint.yml
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Expand Up @@ -11,7 +11,7 @@ jobs:
name: Check out source-code repository

- name: Setup Python
uses: actions/setup-python@v1
uses: actions/setup-python@v4.3.0
with:
python-version: 3.8

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10 changes: 5 additions & 5 deletions .github/workflows/run_tests.yml
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Expand Up @@ -66,7 +66,7 @@ jobs:
uses: actions/checkout@v2.3.4

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2.1.4
uses: actions/setup-python@v4.3.0
with:
python-version: ${{ matrix.python-version }}

Expand Down Expand Up @@ -99,7 +99,7 @@ jobs:
print("::set-output name=result::{}".format(result))
- name: Restore pre-commit cache
uses: actions/cache@v2.1.6
uses: actions/cache@v3.3.1
if: matrix.session == 'pre-commit'
with:
path: ~/.cache/pre-commit
Expand All @@ -113,14 +113,14 @@ jobs:
- name: Upload coverage data
if: always() && matrix.session == 'tests'
uses: "actions/upload-artifact@v2.2.4"
uses: "actions/upload-artifact@v3.1.2"
with:
name: coverage-data
path: ".coverage.*"

- name: Upload documentation
if: matrix.session == 'docs-build'
uses: actions/upload-artifact@v2.2.4
uses: actions/upload-artifact@v3.1.2
with:
name: docs
path: docs/_build
Expand All @@ -133,7 +133,7 @@ jobs:
uses: actions/checkout@v2.3.4

- name: Set up Python 3.8
uses: actions/setup-python@v2.1.4
uses: actions/setup-python@v4.3.0
with:
python-version: 3.8

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2 changes: 1 addition & 1 deletion .github/workflows/sync_project.yml
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Expand Up @@ -10,7 +10,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Setup Python
uses: actions/setup-python@v1
uses: actions/setup-python@v4.3.0
with:
python-version: 3.8

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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Expand Up @@ -44,7 +44,7 @@ repos:
hooks:
- id: prettier
- repo: https://github.com/pycqa/isort
rev: 5.9.3
rev: 5.11.5
hooks:
- id: isort
name: isort (python)
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2 changes: 1 addition & 1 deletion cookietemple.cfg
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@@ -1,5 +1,5 @@
[bumpversion]
current_version = 0.1.4
current_version = 0.1.5

[bumpversion_files_whitelisted]
init_file = ncem/__init__.py
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119 changes: 119 additions & 0 deletions docs/_static/css/custom.css
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.small {
font-size: 55%;
}

div.version {
color: #ffd92c !important;
}

.wy-nav-side {
background: #242335;
}

.wy-side-nav-search {
background-color: #242335;
}

.wy-side-nav-search input[type="text"] {
border-radius: 6px !important;
}

.wy-nav-content {
max-width: 950px;
}

.wy-menu-vertical a {
color: #eceef4;
}

.wy-menu-vertical li.current {
background: #f1f5fb;
}

.wy-menu-vertical li.toctree-l2.current > a {
background: #34377d2e;
}

.wy-menu-vertical li.toctree-l2.current li.toctree-l3 > a {
background: #34377d4a;
}

.wy-menu-vertical li.toctree-l3.current li.toctree-l4 > a {
background: #34377d7d;
}

.wy-menu-vertical a:hover {
background-color: #6b86b0;
}

.wy-menu-vertical li.current a:hover {
background: #bdcde6a3;
}

a {
color: #5b64b1;
}

.rst-content .viewcode-link {
color: #7013e1d9;
}

.highlight {
background: #f1f5fb !important;
}

.rst-content div[class^="highlight"] {
border: 1px solid #e4eaf2;
}

.wy-menu-vertical p.caption {
color: #ffd92c;
}

div.output_subarea.output_html.rendered_html.output_result {
overflow: auto;
}

/* function/class top bar */
html.writer-html5
.rst-content
dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple)
> dt {
color: #404040;
border-top: solid 4px #7013e1d9;
background: #ffd833a8;
}

/* class params */
html.writer-html5
.rst-content
dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple)
dl:not(.field-list)
> dt {
color: #404040;
border-left: solid 4px #7013e1d9;
background: #ffd8338f;
}

/* the other elements, but more specific - leave them be */
code.docutils.literal.notranslate > span[class="pre"] {
font-weight: bold;
color: #404040;
}

/* odd rows in API */
.rst-content table.docutils:not(.field-list) tr:nth-child(2n-1) td {
background-color: #f6f6f3;
}

.rst-content div[class^="highlight"] pre {
padding: 8px;
}

.rst-content .seealso {
background: #fafae2 !important;
}

.rst-content .seealso .admonition-title {
background: #7013e1d9 !important;
}
43 changes: 43 additions & 0 deletions docs/_static/css/dataframe.css
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@@ -0,0 +1,43 @@
/* Pandas dataframe css */
/* Taken from: https://github.com/spatialaudio/nbsphinx/blob/fb3ba670fc1ba5f54d4c487573dbc1b4ecf7e9ff/src/nbsphinx.py#L587-L619 */
/* modified margin-left */

table.dataframe {
border: none !important;
border-collapse: collapse;
border-spacing: 0;
border-color: transparent;
color: black;
font-size: 12px;
table-layout: fixed;
margin-left: 0 !important;
}

table.dataframe thead {
border-bottom: 1px solid black;
vertical-align: bottom;
}

table.dataframe tr,
table.dataframe th,
table.dataframe td {
text-align: right;
vertical-align: middle;
padding: 0.5em 0.5em;
line-height: normal;
white-space: normal;
max-width: none;
border: none;
}

table.dataframe th {
font-weight: bold;
}

table.dataframe tbody tr:nth-child(odd) {
background: #f5f5f5;
}

table.dataframe tbody tr:hover {
background: rgba(66, 165, 245, 0.2);
}
24 changes: 24 additions & 0 deletions docs/_static/css/nbsphinx.css
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div.nbinput.container div.prompt,
div.nboutput.container div.prompt {
display: none;
}

div.nbinput.container div.prompt > div.highlight,
div.nboutput.container div.prompt > div.highlight {
display: none;
}

div.nbinput.container div.input_area div[class*="highlight"] > pre,
div.nboutput.container div.output_area div[class*="highlight"] > pre {
padding: 8px !important;
}

div.nboutput.container div.output_area > div[class^="highlight"] {
background-color: #fafae2 !important;
}

.rst-content .output_area img {
max-width: unset;
width: 100% !important;
height: auto !important;
}
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