Merge pull request #504 from LCSB-BioCore/develop

dev→master 20211105

.gitlab-ci.yml

+
 stages:
-  - generator
-  - test-basic
-  - test-required
-  - documentation
-  - test-additional-v1.5
-  - test-additional-v1.6
+  - test # this checks the viability of the code
+  - documentation-assets # this builds assets to be included in documentation
+  - documentation # this processes the documentation
+  - test-compat # this runs many additional compatibility tests
 
 variables:
-    GIT_STRATEGY: clone
-    DOCKER_DRIVER: overlay2
-    DOCKER_TLS_CERTDIR: ""
+  GIT_STRATEGY: clone
+  DOCKER_DRIVER: overlay2
+  DOCKER_TLS_CERTDIR: ""
+
+#
+# Predefined conditions for triggering jobs
+#
+
+.global_trigger_pull_request: &global_trigger_pull_request
+  rules:
+    - if: $CI_COMMIT_BRANCH == "develop"
+      when: never
+    - if: $CI_COMMIT_BRANCH == "master"
+      when: never
+    - if: $CI_PIPELINE_SOURCE == "external_pull_request_event"
+
+.global_trigger_build_doc: &global_trigger_build_doc
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "external_pull_request_event"
+      when: never
+    - if: $CI_COMMIT_BRANCH == "develop"
+    - if: $CI_COMMIT_TAG =~ /^v/
 
-.global_settings: &global_settings_pull
+.global_trigger_full_tests: &global_trigger_full_tests
   rules:
-   - if: $CI_PIPELINE_SOURCE == "external_pull_request_event"
+    - if: $CI_COMMIT_BRANCH == "develop"
+    - if: $CI_COMMIT_BRANCH == "master"
+    - if: $CI_COMMIT_TAG =~ /^v/
 
-.global_settings: &global_settings_comprehensive
+.global_trigger_compat_tests: &global_trigger_compat_tests
   rules:
-   - if: $CI_COMMIT_BRANCH == "master"
-   - if: $CI_COMMIT_BRANCH == "develop"
-   - if: $CI_COMMIT_TAG =~ /^v/
+    - if: $CI_COMMIT_BRANCH == "master"
+
+#
+# Test environment & platform settings
+#
 
-.global_testing_v15: &global_testing_v15
+.global_julia15: &global_julia15
   variables:
     JULIA_VER: "v1.5.3"
 
-.global_testing_v16: &global_testing_v16
+.global_julia16: &global_julia16
   variables:
     JULIA_VER: "v1.6.0"
 
-# platform-specific test settings
-# --------------------------------------
-
-.global_testing_linux: &global_testing_linux
-  tags:
-   - slave01
+.global_env_linux: &global_env_linux
   script:
     - $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --inline=yes --check-bounds=yes --color=yes --project=@. -e 'import Pkg; Pkg.test(; coverage = true)'
 
-.global_testing_win8: &global_testing_win8
+.global_env_win: &global_env_win
+  script:
+    - $global:LASTEXITCODE = 0 # Note the global prefix.
+    - Invoke-Expression $Env:ARTENOLIS_SOFT_PATH"\julia\"$Env:JULIA_VER"\bin\julia" --inline=yes --check-bounds=yes --color=yes --project=@. -e 'import Pkg; Pkg.test(; coverage = true)'
+    - exit $LASTEXITCODE
+
+.global_env_win8: &global_env_win8
   tags:
     - windows8
+  <<: *global_env_win
 
-.global_testing_win10: &global_testing_win10
+.global_env_win10: &global_env_win10
   tags:
     - windows10
+  <<: *global_env_win
 
-.global_testing_win: &global_testing_win
-  script:
-    - $global:LASTEXITCODE = 0 # Note the global prefix.
-    - Invoke-Expression $Env:ARTENOLIS_SOFT_PATH"\julia\"$Env:JULIA_VER"\bin\julia --inline=yes --check-bounds=yes --color=yes --project=@. -e 'import Pkg; Pkg.test(; coverage = true)'"
-    - exit $LASTEXITCODE
-
-.global_testing_mac: &global_testing_mac
+.global_env_mac: &global_env_mac
   tags:
     - mac
   script:
     - $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/Contents/Resources/julia/bin/julia --inline=yes --check-bounds=yes --color=yes --project=@. -e 'import Pkg; Pkg.test(; coverage = true)'
 
-# Check the format of the code
-# --------------------------------------
+#
+# TESTS
+#
+# The "basic" required test that gets triggered for the basic testing, runs in
+# any available docker and current julia
+#
+
+docker:julia1.6:
+  stage: test
+  image: $CI_REGISTRY/r3/docker/julia-custom
+  script:
+    - julia --check-bounds=yes --inline=yes --project=@. -e "import Pkg; Pkg.test(; coverage = true)"
+  after_script:
+    - julia --project=test/coverage test/coverage/coverage-summary.jl
+  <<: *global_trigger_pull_request
+
+#
+# The required compatibility test to pass on branches&tags before the docs get
+# built & deployed
+#
+
+linux:julia1.5:
+  stage: test
+  tags:
+    - slave01
+  <<: *global_trigger_full_tests
+  <<: *global_julia15
+  <<: *global_env_linux
+
+linux:julia1.6:
+  stage: test
+  tags:
+    - slave02
+  <<: *global_trigger_full_tests
+  <<: *global_julia16
+  <<: *global_env_linux
+
+#
+# Additional platform&environment compatibility tests
+#
+
+windows8:julia1.5:
+  stage: test-compat
+  <<: *global_trigger_compat_tests
+  <<: *global_julia15
+  <<: *global_env_win8
+
+windows10:julia1.5:
+  stage: test-compat
+  <<: *global_trigger_compat_tests
+  <<: *global_julia15
+  <<: *global_env_win10
+
+mac:julia1.5:
+  stage: test-compat
+  <<: *global_trigger_compat_tests
+  <<: *global_julia15
+  <<: *global_env_mac
+
+windows8:julia1.6:
+  stage: test-compat
+  <<: *global_trigger_compat_tests
+  <<: *global_julia16
+  <<: *global_env_win8
+
+windows10:julia1.6:
+  stage: test-compat
+  <<: *global_trigger_compat_tests
+  <<: *global_julia16
+  <<: *global_env_win10
+
+mac:julia1.6:
+  stage: test-compat
+  <<: *global_trigger_compat_tests
+  <<: *global_julia16
+  <<: *global_env_mac
+
+#
+# CODE FORMAT CHECKER
+#
 
 format:
-  stage: test-basic
+  stage: test
   image: docker:19.03.13
   tags:
     - privileged
@@ -100,13 +197,17 @@ format:
             -e GITHUB_COMMENT_FORMAT \
             -e GITHUB_COMMENT \
             cloudposse/github-commenter
-  <<: *global_settings_pull
+  <<: *global_trigger_pull_request
 
-# Documentation history
-# --------------------------------------
+#
+# DOCUMENTATION ASSETS
+#
+# This builds the development history gif using gource.
+#
 
-generator:gource:
-  stage: generator
+documentation-assets:gource:
+  stage: documentation-assets
+  needs: [] # allow faster start
   image: docker:19.03.13
   tags:
     - privileged
@@ -119,123 +220,71 @@ generator:gource:
     - docker run -v "$PWD":/visualization $CI_REGISTRY/r3/docker/gource
   artifacts:
     paths: ['output.gif']
-  <<: *global_settings_comprehensive
-
-# Documentation tests
-# --------------------------------------
-
-doc-tests:v1.6:
-  stage: documentation
+  <<: *global_trigger_build_doc
+
+#
+# DOCUMENTATION TESTS
+#
+# In pull requests, triggered after the tests succeed to avoid unnecessary
+# double failure.  In normal branch testing, these get triggered with normal
+# tests (the error should be visible ASAP). We avoid a separate stage to keep
+# the pipeline parallelizable.
+#
+
+.global_doctests: &global_doctests
   image: $CI_REGISTRY/r3/docker/julia-custom
   script:
     - julia --project=@. -e 'import Pkg; Pkg.instantiate();'
     - julia --project=@. --color=yes test/doctests.jl
-  <<: *global_settings_pull
 
-# Deploy the documentation
-# --------------------------------------
+doc-tests-pr:julia1.6:
+  stage: documentation
+  <<: *global_doctests
+  <<: *global_trigger_pull_request
+
+doc-tests:julia1.6:
+  stage: test
+  <<: *global_doctests
+  <<: *global_trigger_full_tests
+
+#
+# DOCUMENTATION
+#
 
 pages:
   stage: documentation
   dependencies:
-    - generator:gource
+    - documentation-assets:gource
+      # Note: This dependency is also implied by the stage ordering, but let's
+      # be sure. As of Nov 2021, the assets are not used directly, but referred
+      # to externally from the docs.
   image: $CI_REGISTRY/r3/docker/julia-custom
   script:
     # resolve and build packages from the docs/Project.toml file
     - julia --project=docs -e 'using Pkg; Pkg.resolve(); Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate();'
 
-    # deploy doc (without git history)
+    # build and deploy docs (this doesn't upload the gource animation asset)
     - julia --project=docs --color=yes docs/make.jl
 
-    # move to the directory picked up by Gitlab pages (with git history)
+    # move to the directory to be picked up by Gitlab pages (with assets)
     - mv docs/build public
   artifacts:
     paths:
       - public
-  <<: *global_settings_comprehensive
-
-# Test Docker run with Julia v1.6
-# --------------------------------------
+  <<: *global_trigger_build_doc
 
-docker:v1.6:
-  stage: test-basic
-  image: $CI_REGISTRY/r3/docker/julia-custom
-  script:
-    - julia --check-bounds=yes --inline=yes --project=@. -e "import Pkg; Pkg.test(; coverage = true)"
-  after_script:
-    - julia --project=test/coverage test/coverage/coverage-summary.jl
-  <<: *global_settings_pull
-
-# Test Julia v1.5
-# --------------------------------------
-
-linux:v1.5:
-  stage: test-required
-  <<: *global_settings_comprehensive
-  <<: *global_testing_v15
-  <<: *global_testing_linux
-
-windows10:v1.5:
-  stage: test-additional-v1.5
-  <<: *global_settings_comprehensive
-  <<: *global_testing_v15
-  <<: *global_testing_win10
-  <<: *global_testing_win
-
-windows8:v1.5:
-  stage: test-additional-v1.5
-  <<: *global_settings_comprehensive
-  <<: *global_testing_v15
-  <<: *global_testing_win8
-  <<: *global_testing_win
-
-mac:v1.5:
-  stage: test-additional-v1.5
-  <<: *global_settings_comprehensive
-  <<: *global_testing_v15
-  <<: *global_testing_mac
-
-# Test Julia v1.6
-# --------------------------------------
-
-linux:v1.6:
-  stage: test-additional-v1.6
-  needs: ["linux:v1.5"]
-  <<: *global_settings_comprehensive
-  <<: *global_testing_v16
-  <<: *global_testing_linux
-
-windows10:v1.6:
-  stage: test-additional-v1.6
-  needs: ["windows10:v1.5"]
-  <<: *global_settings_comprehensive
-  <<: *global_testing_v16
-  <<: *global_testing_win10
-  <<: *global_testing_win
-
-windows8:v1.6:
-  stage: test-additional-v1.6
-  needs: ["windows8:v1.5"]
-  <<: *global_settings_comprehensive
-  <<: *global_testing_v16
-  <<: *global_testing_win8
-  <<: *global_testing_win
-
-mac:v1.6:
-  stage: test-additional-v1.6
-  needs: ["mac:v1.5"]
-  <<: *global_settings_comprehensive
-  <<: *global_testing_v16
-  <<: *global_testing_mac
-
-# Trigger test pipelines in external repo
-# --------------------------------------
+#
+# EXTERNAL REPOSITORIES
+#
+# This trigger the test pipeline in external repo as defined by gitlab
+# variables.
+#
 
 trigger:
-  stage: test-required
+  stage: test-compat
   image: curlimages/curl
   tags:
     - privileged
   script:
     - curl --silent --output /dev/null -X POST -F token=$EXTERNAL_REPO_TOKEN -F ref=$EXTERNAL_REPO_BRANCH $EXTERNAL_REPO
-  <<: *global_settings_comprehensive
+  <<: *global_trigger_full_tests

README.md

@@ -18,7 +18,7 @@
 [cov-url]: https://codecov.io/gh/LCSB-BioCore/COBREXA.jl
 
 [contrib-img]: https://img.shields.io/badge/contributions-start%20here-green
-[contrib-url]: https://lcsb-biocore.github.io/COBREXA.jl/dev/howToContribute/
+[contrib-url]: https://lcsb-biocore.github.io/COBREXA.jl/stable/howToContribute/
 
 [repostatus-url]: https://www.repostatus.org/#active
 [repostatus-img]: https://www.repostatus.org/badges/latest/active.svg

docs/make.jl

@@ -5,8 +5,9 @@ using COBREXA
 # some settings
 dev_docs_folder = "dev"
 pages_branch = "gh-pages"
-github_repo_slug = "LCSB-BioCore/COBREXA.jl"
-delete!(ENV, "GITHUB_REPOSITORY")
+
+# This must match the repo slug on github!
+github_repo_slug = ENV["CI_PROJECT_NAMESPACE"] * "/" * ENV["CI_PROJECT_NAME"]
 
 # generate notebooks
 notebooks_path = joinpath(@__DIR__, "src", "notebooks")
@@ -15,8 +16,6 @@ notebooks_basenames = filter(x -> endswith(x, ".jl"), readdir(notebooks_path))
 notebooks = joinpath.(notebooks_path, notebooks_basenames)
 notebooks_outdir = joinpath(@__DIR__, "src", "notebooks")
 
-
-
 for notebook in notebooks
     Literate.markdown(
         notebook,
@@ -51,12 +50,19 @@ cp(
     force = true,
 )
 
+# a helper for sourcing the documentation files from directories
 find_mds(path) =
     joinpath.(
         Ref(path),
         filter(x -> endswith(x, ".md"), readdir(joinpath(@__DIR__, "src", path))),
     )
 
+# Documenter tries to guess the repo slug from git remote URL but that doesn't
+# work really well here, this is the only fallback. If this breaks, "Edit on
+# GitHub" links will stop working. (See Documenter.jl source in
+# src/Utilities/Utilities.jl, in November 2021 it was around line 500) -mk
+ENV["TRAVIS_REPO_SLUG"] = github_repo_slug
+
 # build the docs
 makedocs(
     modules = [COBREXA],
@@ -73,24 +79,22 @@ makedocs(
     pages = [
         "Home" => "index.md",
         "User guide" => [
-            "Quickstart tutorials" => vcat(
-                "Detailed tutorial listing" => "tutorials.md",
-                find_mds("tutorials"),
-            ),
-            "Advanced tutorials" => vcat(
-                "Detailed tutorial listing" => "advanced.md",
-                find_mds("advanced"),
-            ),
-            "Examples and notebooks" => vcat(
-                "Detailed notebook listing" => "notebooks.md",
-                find_mds("notebooks"),
-            ),
+            "Quickstart tutorials" =>
+                vcat("All tutorials" => "tutorials.md", find_mds("tutorials")),
+            "Advanced tutorials" =>
+                vcat("All advanced tutorials" => "advanced.md", find_mds("advanced")),
+            "Examples and notebooks" =>
+                vcat("All notebooks" => "notebooks.md", find_mds("notebooks")),
         ],
-        "API reference" => vcat("Contents" => "functions.md", find_mds("functions")),
+        "Types and functions" => vcat("Contents" => "functions.md", find_mds("functions")),
         "How to contribute" => "howToContribute.md",
     ],
 )
 
+# remove the workaround (this would cause deploydocs() to get confused and try
+# to deploy the travis way)
+delete!(ENV, "TRAVIS_REPO_SLUG")
+
 # replace the "edit this" links for the generated documentation
 function replace_in_doc(filename, replacement)
     contents = open(f -> read(f, String), joinpath(@__DIR__, "build", filename))
@@ -142,6 +146,5 @@ deploydocs(
     repo = "github.com/$github_repo_slug.git",
     target = "build",
     branch = pages_branch,
-    push_preview = true,
     devbranch = "develop",
 )

docs/src/assets/hhu.svg

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 <svg
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-   xmlns:cc="http://creativecommons.org/ns#"
-   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-   xmlns:svg="http://www.w3.org/2000/svg"
-   xmlns="http://www.w3.org/2000/svg"
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    xml:space="preserve"
-   width="1188.2295"
-   height="588.8277"
-   viewBox="0 0 1188.2295 588.8277"
+   width="131.64713"
+   height="64"
+   viewBox="0 0 131.64713 64"
    sodipodi:docname="hhu.svg"
-   inkscape:version="1.0.2 (e86c870879, 2021-01-15)"><metadata
+   inkscape:version="1.1.1 (3bf5ae0d25, 2021-09-20)"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:dc="http://purl.org/dc/elements/1.1/"><metadata
      id="metadata8"><rdf:RDF><cc:Work
          rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
-           rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><defs
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" /></cc:Work></rdf:RDF></metadata><defs
      id="defs6"><clipPath
        clipPathUnits="userSpaceOnUse"
        id="clipPath18"><path
@@ -32,25 +32,27 @@
      inkscape:pageopacity="0"
      inkscape:pageshadow="2"
      inkscape:window-width="1920"
-     inkscape:window-height="1047"
+     inkscape:window-height="1166"
      id="namedview4"
      showgrid="false"
-     fit-margin-top="150"
+     fit-margin-top="16"
      fit-margin-left="0"
      fit-margin-right="0"
-     fit-margin-bottom="150"
-     inkscape:zoom="0.54223161"
-     inkscape:cx="547.04525"
-     inkscape:cy="254.34294"
+     fit-margin-bottom="16"
+     inkscape:zoom="3.0334871"
+     inkscape:cx="137.46556"
+     inkscape:cy="40.382568"
      inkscape:window-x="0"
-     inkscape:window-y="33"
+     inkscape:window-y="2194"
      inkscape:window-maximized="1"
-     inkscape:current-layer="g10" /><g
+     inkscape:current-layer="g10"
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      inkscape:label="Logo_HHU_+Name_horizontal_rgb_+Safezone"
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-       id="g906"><g
+     transform="matrix(1.3333333,0,0,-1.3333333,-178.53093,453.69159)"><g
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@@ -66,7 +68,8 @@
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