Merge pull request #154 from theislab/development

update docs and python versions

.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;
+}