Merge pull request #122 from LCSB-BioCore/develop

Regular merge of develop
LCSB-BioCore · Apr 19, 2020 · c19f5d5 · c19f5d5
2 parents 9b37c3a + 3614286
commit c19f5d5
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Showing 6 changed files with 50 additions and 21 deletions.
diff --git a/.artenolis.yml b/.artenolis.yml
@@ -10,7 +10,6 @@ script:
 
     # change to the current directory
     - cd $CURRENT_DIR
-
     - echo $NODE_LABELS
 
     # rename the cloned folder
@@ -26,19 +25,6 @@ after_success:
         $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --color=yes -e 'using Coverage; Codecov.submit(process_folder())';
       fi
 
-    # deploy documentation
-    - if [[ "$ARCH" == "Linux" && "$JENKINS_PULL_REQUEST" != "True" && "$JULIA_VER" = "v1.2.0" ]]; then
-        export TRAVIS_BRANCH=$GIT_BRANCH;
-        export TRAVIS_PULL_REQUEST=false;
-        var=$GIT_URL; export TRAVIS_REPO_SLUG=${var:8:${#var}};
-        export TRAVIS_OS_NAME=$label;
-        export TRAVIS_JULIA_VERSION=$JULIA_VER;
-        export TRAVIS_TAG=$GIT_TAG_NAME;
-        cd $CURRENT_DIR;
-        $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()';
-        $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --project=docs/ docs/make.jl;
-      fi
-
 after_script:
     # clean up the build directory
     - cd .. && rm -rf GigaSOM
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -4,7 +4,9 @@
 
 ## How can I contribute?
 
-### Report a bug or suggest an enhancement
+A complete technical guide on how to get started contributing is given [here](https://lcsb-biocore.github.io/GigaSOM.jl/stable/howToContribute/).
+
+## How to report a bug or suggest an enhancement
 
 Please use the [GitHub issue tracker](https://github.com/LCSB-BioCore/GigaSOM.jl/issues) to report any problems with the software, and discuss any potential questions about GigaSOM use.
 
@@ -20,7 +22,7 @@ information it asks for helps us resolve issues faster.
 
 If reporting issues, please do not forget to include a description of conditions under which the issue occurs; preferably a code snippet that can be run separately (sometimes termed "minimal crashing example").
 
-### Pull Requests
+## How to submit a pull request (PR)?
 
 Please follow these steps to have your contribution considered by the maintainers:
 
@@ -29,4 +31,4 @@ Please follow these steps to have your contribution considered by the maintainer
 3. After you submit your pull request, verify that all status checks are passing
 
 After you submitted a pull request, a label might be assigned that allows us
-to track and manage issues and pull requests.
+to track and manage issues and pull requests.
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -0,0 +1,24 @@
+# ref: https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#GitHub-Actions-1
+name: Documentation
+
+on:
+  push:
+    branches:
+      - develop
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: 1.3
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+        run: julia --project=docs/ docs/make.jl
diff --git a/Project.toml b/Project.toml
@@ -1,6 +1,6 @@
 name = "GigaSOM"
 uuid = "a03a9c34-069e-5582-a11c-5c984cab887c"
-version = "0.4.0"
+version = "0.4.1"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

diff --git a/docs/make.jl b/docs/make.jl
@@ -26,6 +26,6 @@ deploydocs(
     repo = "github.com/LCSB-BioCore/GigaSOM.jl.git",
     target = "build",
     branch = "gh-pages",
-    devbranch = "origin/develop",
+    devbranch = "develop",
     versions = "stable" => "v^",
     )
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -5,9 +5,26 @@
 
 GigaSOM.jl allows painless analysis of huge-scale clinical studies, scaling down the software limitations that usually prevent work with large datasets. It can be viewed as a work-alike of FlowSOM, suitable for loading billions of cells and running the analyses in parallel on distributed computer clusters, to gain speed. Most importantly, GigaSOM.jl scales horizontally -- data volume limitations and memory limitations can be solved just by adding more computers to the cluster. That makes it extremely easy to exploit HPC environments, which are becoming increasingly common in computational biology.
 
+```@raw html
+<style type="text/css">
+.evo {
+    width: 250px;
+    margin: 1em;
+    border-radius: 50%;
+    -webkit-border-radius: 50%;
+    -moz-border-radius: 50%;
+}
+</style>
+<div align="center">
+    <img class="evo" src="https://prince.lcsb.uni.lu/GigaSOM.jl/img/evolution.gif">
+    <br/>
+    <b>Evolution of the GigaSOM.jl repository (2019-2020)</b>
+</div>
+```
+
 ### Features
 
-- Horizontal scalability to literal giga-scale datasets (10^9 cells!)
+- Horizontal scalability to literal giga-scale datasets (``10^9`` cells!)
 - HPC-ready, support for e.g. Slurm
 - Standard support for distributed loading, scaling and transforming the FCS3 files
 - Batch-SOM based GigaSOM algorithm for clustering
@@ -47,4 +64,4 @@ If you want to contribute, please read these guidelines first:
 
 ```@contents
 Pages = ["howToContribute.md"]
-```
+```