Improve documentation

docker/requirements.txt

@@ -1,42 +1,124 @@
+aiobotocore==2.5.4
+aiohttp==3.8.6
+aioitertools==0.11.0
+aiosignal==1.3.1
+alabaster==0.7.13
 anndata==0.8.0
-apeer-ometiff-library==1.8.2
 asciitree==0.3.3
-cached-property==1.5.2
-cloudpickle==2.0.0
-dask==2022.2.0
-fasteners==0.17.3
+async-timeout==4.0.3
+attrs==23.1.0
+Babel==2.13.0
+black==23.10.0
+botocore==1.31.17
+certifi==2023.7.22
+cffi==1.16.0
+cfgv==3.4.0
+charset-normalizer==3.3.0
+click==8.1.7
+cloudpickle==3.0.0
+contourpy==1.1.1
+coverage==7.3.2
+cycler==0.12.1
+dask==2023.5.0
+distlib==0.3.7
+docutils==0.18.1
+elementpath==4.1.5
+exceptiongroup==1.1.3
+fasteners==0.19
+filelock==3.12.4
 fire==0.5.0
-fsspec==2022.1.0
-h5py==3.6.0
-importlib-metadata==4.11.1
-locket==0.2.1
-matplotlib==3.6
-natsort==8.1.0
-numcodecs==0.9.1
-numpy==1.21.5
-ome_zarr==0.2.1
-packaging==21.3
-pandas==1.3.5
-partd==1.2.0
-pre_commit==2.20.0
-pyparsing==3.0.7
-pytest==7.1.2
-pytest-cov==3.0.0
+fonttools==4.43.1
+frozenlist==1.4.0
+fsspec==2023.9.2
+h5py==3.10.0
+identify==2.5.30
+idna==3.4
+imageio==2.31.5
+imagesize==1.4.1
+importlib-metadata==6.8.0
+importlib-resources==6.1.0
+iniconfig==2.0.0
+Jinja2==3.1.2
+jmespath==1.0.1
+joblib==1.3.2
+jsonschema==4.19.1
+jsonschema-specifications==2023.7.1
+kiwisolver==1.4.5
+lazy_loader==0.3
+llvmlite==0.41.1
+locket==1.0.0
+MarkupSafe==2.1.3
+matplotlib==3.7.3
+multidict==6.0.4
+mypy-extensions==1.0.0
+natsort==8.4.0
+negspy==0.2.24
+networkx==3.1
+nodeenv==1.8.0
+numba==0.58.1
+numcodecs==0.12.1
+numpy==1.24.4
+ome-zarr==0.2.1
+packaging==23.2
+pandas==2.0.3
+partd==1.4.1
+pathspec==0.11.2
+patsy==0.5.3
+Pillow==10.1.0
+pkgutil_resolve_name==1.3.10
+platformdirs==3.11.0
+pluggy==1.3.0
+pre-commit==3.5.0
+pycparser==2.21
+Pygments==2.16.1
+pynndescent==0.5.10
+pyparsing==3.1.1
+pytest==7.4.2
+pytest-cov==4.1.0
 python-dateutil==2.8.2
-pytz==2021.3
+pytz==2023.3.post1
 pyvips==2.2.1
-PyYAML==6.0
-regex==2022.7.25
-scanpy==1.9.1
-scikit-image==0.19.3
-scipy==1.7.3
-Shapely==1.8.0
+PyWavelets==1.4.1
+PyYAML==6.0.1
+referencing==0.30.2
+regex==2023.10.3
+requests==2.31.0
+rpds-py==0.10.6
+s3fs==2023.9.2
+scanpy==1.9.5
+scikit-image==0.21.0
+scikit-learn==1.3.1
+scipy==1.10.1
+seaborn==0.13.0
+session-info==1.0.0
 six==1.16.0
-tifffile==2021.11.2
-toolz==0.11.2
-typing-extensions==4.1.1
-xlrd==1.2.0
-xmlschema==1.11.3
-zarr==2.11.0
-zipp==3.7.0
-vitessce==3.0.4
+snowballstemmer==2.2.0
+Sphinx==7.1.2
+sphinx-rtd-theme==1.3.0
+sphinxcontrib-applehelp==1.0.4
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.1
+sphinxcontrib-jquery==4.1
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+statsmodels==0.14.0
+stdlib-list==0.9.0
+tbb==2021.10.0
+termcolor==2.3.0
+threadpoolctl==3.2.0
+tifffile==2023.7.10
+tomli==2.0.1
+toolz==0.12.0
+tqdm==4.66.1
+typing_extensions==4.8.0
+tzdata==2023.3
+umap-learn==0.5.4
+urllib3==1.26.18
+virtualenv==20.24.5
+vitessce==3.1.1
+wrapt==1.15.0
+xmlschema==2.5.0
+yarl==1.9.2
+zarr==2.16.1
+zipp==3.17.0

environment.yaml

@@ -0,0 +1,45 @@
+name: webatlas
+channels:
+  - conda-forge
+dependencies:
+  - colorama=0.4.6
+  - dask=2023.9.0
+  - fire=0.5.0
+  - fsspec=2023.9.0
+  - h5py=3.9.0
+  - imagecodecs=2023.8.12
+  - markupsafe=2.1.3
+  - nodejs=20.5.1
+  - numba=0.57.1
+  - numcodecs=0.11.0
+  - numpy=1.24.4
+  - openjdk=11
+  - openjpeg=2.5.0
+  - pandas=2.1.0
+  - pip=23.2.1
+  - python=3.10.12
+  - python-dateutil=2.8.2
+  - python-tzdata=2023.3
+  - python_abi=3.10
+  - pyvips=2.2.1
+  - regex=2023.8.8
+  - scanpy=1.9.4
+  - scikit-image=0.21.0
+  - scikit-learn=1.3.0
+  - scipy=1.11.2
+  - setuptools=68.1.2
+  - shapely=2.0.1
+  - snappy=1.1.10
+  - tifffile=2023.8.30
+  - umap-learn=0.5.3
+  - wheel=0.41.2
+  - zarr=2.16.1
+  - bioconda::nextflow=23.04.1
+  - ome::bioformats2raw=0.7.0
+  - ome::bioformats2raw-libs=0.7.0
+  - ome::raw2ometiff=0.5.0=0
+  - ome::raw2ometiff-libs=0.5.0=0
+  - pip:
+      - apeer-ometiff-library==1.9.0
+      - ome-zarr==0.2.1
+      - vitessce==3.0.7

nextflow.config

@@ -1,15 +1,18 @@
-singularity.enabled = false
-singularity.autoMounts = false
+profiles {
 
-docker.enabled = true
-process.container = 'haniffalab/webatlas-pipeline:0.3.2'
+  conda { 
+    conda.enabled = true
+    process.conda = "$baseDir/environment.yaml" 
+  }
 
-// see https://www.nextflow.io/docs/latest/config.html#scope-aws
-aws {
-  accessKey = '[YOUR-ACCESS-KEY]'
-  secretKey = '[YOUR-SECRET-KEY]'
-  client {
-        endpoint = 'https://cog.sanger.ac.uk'
-        signerOverride = "S3SignerType"
+  docker { 
+    docker.enabled = true
+    process.container = 'haniffalab/webatlas-pipeline:0.3.2'
+  }
+
+  singularity { 
+    singularity.enabled = false
+    singularity.autoMounts = false
   }
-}
+
+}

sphinx/README.md

@@ -0,0 +1,12 @@
+Tested with Python 3.8
+
+From the project root directory:
+
+```
+python -m venv venv
+. venv/bin/activate
+pip install --upgrade pip
+pip install -r ./docker/requirements.txt 
+cd sphinx/
+make html
+```

sphinx/_static/css/custom.css

@@ -1,7 +1,25 @@
 .rst-content .code-block-caption {
     text-align: left;
-    padding: 2px;
+    font-weight: 700;
+    display: block;
+    color: #fff;
+    background: #6ab0de;
+    padding: 6px 12px;
 }
+.rst-content div[class^=highlight] {
+    margin-top: 0;
+}
+.admonition.shell-output {
+    font-size: 85%;
+    line-height: 1;
+} 
+.admonition.shell-output .admonition-title:before {
+    content: None;
+}
+.admonition.shell-output .admonition-title {
+    font-style: italic;
+}
+
 
 .citation {
     font-weight: bold;