Development

.cookietemple.yml

@@ -15,5 +15,5 @@ full_name: Anna Schaar
 email: [email protected]
 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

.github/release-drafter.yml

@@ -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:

.github/workflows/build_package.yml

@@ -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 }}
 

.github/workflows/main_master_branch_protection.yml

@@ -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

.github/workflows/publish_docs.yml

@@ -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
 

.github/workflows/publish_package.yml

@@ -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"
 
@@ -31,7 +31,7 @@ jobs:
  - name: Publish package on PyPI
  uses: pypa/[email protected]
  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 }}

.github/workflows/run_cookietemple_lint.yml

@@ -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
 

.github/workflows/run_tests.yml

@@ -66,7 +66,7 @@ jobs:
  uses: actions/[email protected]
 
  - 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 }}
 
@@ -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
@@ -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
@@ -133,7 +133,7 @@ jobs:
  uses: actions/[email protected]
 
  - 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
 

.github/workflows/sync_project.yml

@@ -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
 

.pre-commit-config.yaml

@@ -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)

cookietemple.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.4
+current_version = 0.1.5
 
 [bumpversion_files_whitelisted]
 init_file = ncem/__init__.py

docs/_static/css/custom.css

@@ -0,0 +1,119 @@
+.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;
+}

docs/_static/css/dataframe.css

@@ -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);
+}

docs/_static/css/nbsphinx.css

@@ -0,0 +1,24 @@
+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;
+}