Remove redundant jobs.

Remove distinction between jobs that do and do not stage a build of the
gmxapi Python package in the build tree for API breakage testing and
full documentation builds.

Set a default CMake flag of "-DGMX_PYTHON_PACKAGE=ON" and install some
Python package dependencies with the default EXTRA_INSTALLS. The extra
installs will go away in the near future with updated Docker images.

Removes (up to) 12 jobs from the pipeline.

Change-Id: I13a60b7323ac0bf240f00b3b1360bedd2886e902

diff --git a/admin/gitlab-ci/archive.gitlab-ci.yml b/admin/gitlab-ci/archive.gitlab-ci.yml
index e1cc6cea431233d512f65247209444c0e06de8ca..a41d6c5d90c3f5576403293458109595883e4130 100644 (file)
--- a/admin/gitlab-ci/archive.gitlab-ci.yml
+++ b/admin/gitlab-ci/archive.gitlab-ci.yml
@@ -338,7 +338,6 @@ release-verify:
 webpage-archive-release:
   extends:
     - .build-docs-webpage
-    - .configure-gmxapi-template
   stage: release-deploy
   only:
     refs:

diff --git a/admin/gitlab-ci/documentation.gitlab-ci.yml b/admin/gitlab-ci/documentation.gitlab-ci.yml
index 2731ef36fed7e1e87362b5d0e213b8533e5686e0..72f1f3748110f02a7cfded56c98ee79f045a9e79 100644 (file)
--- a/admin/gitlab-ci/documentation.gitlab-ci.yml
+++ b/admin/gitlab-ci/documentation.gitlab-ci.yml
@@ -1,8 +1,5 @@
 # Build documentation and web page.
 .documentation-before-script-template:
-  variables:
-    EXTRA_INSTALLS: ""
-
   before_script:
     - echo $EXTRA_INSTALLS
     - time apt-get -qq update
@@ -17,6 +14,8 @@
   # TODO this should be organized more like the current documentation.py script
   image: gromacs/ci-docs-clang:master
   stage: configure-build
+  extends:
+    - .variables:default
   only:
     refs:
       - web
@@ -34,7 +33,6 @@
     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
-    CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
   script:
     - if [[ ! -z $GROMACS_RELEASE && $GROMACS_RELEASE == "true" ]] ; then
       REL_OPTION="-DGMX_BUILD_TARBALL=ON" ;
@@ -85,6 +83,8 @@
   # TODO this should be organized more like the current documentation.py script
   image: gromacs/ci-docs-clang:master
   stage: release-configure
+  extends:
+    - .variables:default
   variables:
     KUBERNETES_CPU_LIMIT: 1
     KUBERNETES_CPU_REQUEST: 1
@@ -96,7 +96,6 @@
     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
-    CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
     RELEASE_BUILD_DIR: release-doc-builds
     RELEASE_SOURCE: release-source-from-tarball
     RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
@@ -217,20 +216,6 @@ configure-docs:
     variables:
       - $GROMACS_RELEASE
 
-configure-docs-gmxapi:
-  extends:
-    - .configure-docs
-    - .configure-gmxapi-template
-  needs:
-    - job: simple-build
-      artifacts: false
-  variables:
-    BUILD_DIR: build-docs-gmxapi
-    CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
-  except:
-    variables:
-      - $GROMACS_RELEASE
-
 .build-docs-binary-template:
   # Built by admin/dockerfiles/ci-docs-clang
   # TODO this should be organized more like the current documentation.py script
@@ -323,23 +308,6 @@ build-docs:
     variables:
       - $GROMACS_RELEASE
 
-build-docs-gmxapi:
-  extends:
-    - .build-docs-binary
-    - .gmxapi-extra-installs
-  stage: documentation
-  needs:
-    - job: simple-build
-      artifacts: false
-    - job: configure-docs-gmxapi
-      artifacts: true
-  variables:
-    BUILD_DIR: build-docs-gmxapi
-  except:
-    variables:
-      - $GROMACS_RELEASE
-
-
 # The manual build is built separately so that errors in converting
 # Sphinx to LaTeX and compiling can always be found in the
 # all-output.txt file, while avoiding many thousands of lines of spam
@@ -363,26 +331,9 @@ webpage:
     variables:
       - $GROMACS_RELEASE
 
-webpage-gmxapi:
-  extends:
-    - .build-docs-webpage
-    - .gmxapi-extra-installs
-  stage: post-test
-  needs:
-    - job: build-docs-gmxapi
-      artifacts: true
-    - job: run-check-source
-      artifacts: false
-  variables:
-    BUILD_DIR: build-docs-gmxapi
-  except:
-    variables:
-      - $GROMACS_RELEASE
-
 webpage-nightly:
   extends:
     - .build-docs-webpage
-    - .configure-gmxapi-template
   stage: nightly-deploy
   only:
     - web
@@ -396,10 +347,10 @@ webpage-nightly:
       artifacts: false
     - job: linkchecker
       artifacts: false
-    - job: webpage-gmxapi
+    - job: webpage
       artifacts: true
   variables:
-    BUILD_DIR: build-docs-gmxapi
+    BUILD_DIR: build-docs
   script:
     - tar czf webpage.tar.gz $BUILD_DIR/docs/html/
   artifacts:
@@ -410,7 +361,6 @@ webpage-nightly:
 webpage-configure-release:
   extends:
     - .configure-docs-release
-    - .configure-gmxapi-template
   cache: {}
   only:
     refs:
@@ -430,7 +380,6 @@ webpage-configure-release:
 webpage-binary-release:
   extends:
     - .build-docs-binary
-    - .gmxapi-extra-installs
   stage: release-build
   needs:
     - job: webpage-configure-release
@@ -448,7 +397,6 @@ webpage-binary-release:
 webpage-build-release:
   extends:
     - .build-docs-webpage
-    - .configure-gmxapi-template
   dependencies:
     - webpage-binary-release
     - webpage-configure-release

diff --git a/admin/gitlab-ci/global.gitlab-ci.yml b/admin/gitlab-ci/global.gitlab-ci.yml
index c9319c2a3294d1d48572ce92311a787f1b28dbd2..730a532836ff008eddcae6800f51d6035bd53eff 100644 (file)
--- a/admin/gitlab-ci/global.gitlab-ci.yml
+++ b/admin/gitlab-ci/global.gitlab-ci.yml
@@ -12,7 +12,9 @@
     CACHE_FALLBACK_KEY: "$CI_JOB_NAME-$CI_JOB_STAGE-master"
     BUILD_DIR: build
     INSTALL_DIR: install
-    EXTRA_INSTALLS: ""
+    CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=ON"
+    EXTRA_INSTALLS: "python3-dev python3-setuptools python3-pip python3-pytest"
+# TODO: Get these from updated Docker images.
 
 # Behavioral templates
 
@@ -23,17 +25,6 @@
     paths:
       - ccache/
 
-
-.gmxapi-extra-installs:
-  variables:
-    EXTRA_INSTALLS: python3-dev python3-networkx python3-setuptools python3-mpi4py python3-numpy python3-pip python3-pytest
-
-.configure-gmxapi-template:
-  extends:
-    - .gmxapi-extra-installs
-  variables:
-    CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=ON"
-
 # Tool chains
 
 .use-cuda:

diff --git a/admin/gitlab-ci/gromacs.gitlab-ci.yml b/admin/gitlab-ci/gromacs.gitlab-ci.yml
index 90a33670c154fb95a30f7590478d22514eaaacc6..64af06e4424ba0e08bd12bd0aea5443414413d28 100644 (file)
--- a/admin/gitlab-ci/gromacs.gitlab-ci.yml
+++ b/admin/gitlab-ci/gromacs.gitlab-ci.yml
@@ -108,7 +108,6 @@ simple-build:
     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
-    CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
   script:
     - echo $CMAKE_COMPILER_SCRIPT
     - echo $CMAKE_EXTRA_OPTIONS
@@ -161,7 +160,6 @@ simple-build:
     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
-    CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
     RELEASE_BUILD_DIR: release-builds
     RELEASE_SOURCE: release-source-from-tarball
     RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
@@ -314,38 +312,6 @@ gromacs:gcc-7-double:release:configure:
     - package-regressiontests-release
     - prepare-release-version
 
-gromacs:gcc-7:configure-gmxapi:
-  extends:
-    - .gromacs:base:configure
-    - .configure-gmxapi-template
-    - .use-gcc7
-  needs:
-    - job: simple-build
-      artifacts: false
-  except:
-    variables:
-      - $GROMACS_RELEASE
-
-gromacs:gcc-7:release:configure-gmxapi:
-  extends:
-    - .gromacs:base:release:configure
-    - .configure-gmxapi-template
-    - .use-gcc7
-  cache: {}
-  variables:
-    RELEASE_BUILD_DIR: release-builds-gcc
-  only:
-    refs:
-      - web
-      - schedules
-      - triggers
-    variables:
-      - $GROMACS_RELEASE
-  dependencies:
-    - package-archive-release
-    - package-regressiontests-release
-    - prepare-release-version
-
 gromacs:gcc-8:configure:
   extends:
     - .gromacs:base:configure
@@ -381,6 +347,9 @@ gromacs:gcc-8-cuda-10.2:configure:
     - .gromacs:base:configure
     - .use-cuda
     - .use-gcc8:cuda-10.2
+  variables:
+    CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
+  # TODO: Enable GMX_PYTHON_PACKAGE when dependencies are in Docker image.
   needs:
     - job: simple-build
       artifacts: false
@@ -435,38 +404,6 @@ gromacs:clang-7:release:configure:
     - package-regressiontests-release
     - prepare-release-version
 
-gromacs:clang-7:configure-gmxapi:
-  extends:
-    - .gromacs:base:configure
-    - .configure-gmxapi-template
-    - .use-clang7
-  needs:
-    - job: simple-build
-      artifacts: false
-  except:
-    variables:
-      - $GROMACS_RELEASE
-
-gromacs:clang-7:release:configure-gmxapi:
-  extends:
-    - .gromacs:base:release:configure
-    - .configure-gmxapi-template
-    - .use-clang7
-  cache: {}
-  variables:
-    RELEASE_BUILD_DIR: release-builds-clang
-  only:
-    refs:
-      - web
-      - schedules
-      - triggers
-    variables:
-      - $GROMACS_RELEASE
-  dependencies:
-    - package-archive-release
-    - package-regressiontests-release
-    - prepare-release-version
-
 gromacs:clang-8:configure:
   extends:
     - .gromacs:base:configure
@@ -590,22 +527,6 @@ gromacs:gcc-7-double:build:
     variables:
       - $GROMACS_RELEASE
 
-gromacs:gcc-7:build-gmxapi:
-  extends:
-    - .gromacs:base:build
-    - .use-ccache
-    - .variables:default
-    - .gmxapi-extra-installs
-    - .use-gcc7
-  needs:
-    - job: simple-build
-      artifacts: false
-    - job: gromacs:gcc-7:configure-gmxapi
-      artifacts: true
-  except:
-    variables:
-      - $GROMACS_RELEASE
-
 gromacs:gcc-7-double:release:build:
   extends:
     - .gromacs:base:build
@@ -626,27 +547,6 @@ gromacs:gcc-7-double:release:build:
     variables:
       - $GROMACS_RELEASE
 
-gromacs:gcc-7:release:build-gmxapi:
-  extends:
-    - .gromacs:base:build
-    - .use-ccache
-    - .variables:default
-    - .gmxapi-extra-installs
-    - .use-gcc7
-  stage: release-build
-  variables:
-    BUILD_DIR: release-builds-gcc
-  needs:
-    - job: gromacs:gcc-7:release:configure-gmxapi
-      artifacts: true
-  only:
-    refs:
-      - web
-      - schedules
-      - triggers
-    variables:
-      - $GROMACS_RELEASE
-
 gromacs:gcc-8:build:
   extends:
     - .gromacs:base:build
@@ -689,6 +589,9 @@ gromacs:gcc-8-cuda-10.2:build:
     - .variables:default
     - .use-cuda
     - .use-gcc8:cuda-10.2
+  variables:
+    CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
+  # TODO: Enable GMX_PYTHON_PACKAGE when dependencies are in Docker image.
   needs:
     - job: simple-build
       artifacts: false
@@ -748,43 +651,6 @@ gromacs:clang-7:release:build:
     variables:
       - $GROMACS_RELEASE
 
-gromacs:clang-7:build-gmxapi:
-  extends:
-    - .gromacs:base:build
-    - .use-ccache
-    - .variables:default
-    - .gmxapi-extra-installs
-    - .use-clang7
-  needs:
-    - job: simple-build
-      artifacts: false
-    - job: gromacs:clang-7:configure-gmxapi
-      artifacts: true
-  except:
-    variables:
-      - $GROMACS_RELEASE
-
-gromacs:clang-7:release:build-gmxapi:
-  extends:
-    - .gromacs:base:build
-    - .use-ccache
-    - .variables:default
-    - .gmxapi-extra-installs
-    - .use-clang7
-  stage: release-build
-  variables:
-    BUILD_DIR: release-builds-clang
-  needs:
-    - job: gromacs:clang-7:release:configure-gmxapi
-      artifacts: true
-  only:
-    refs:
-      - web
-      - schedules
-      - triggers
-    variables:
-      - $GROMACS_RELEASE
-
 gromacs:clang-8:build:
   extends:
     - .gromacs:base:build
@@ -948,41 +814,6 @@ gromacs:gcc-7-double:release:test:
     variables:
       - $GROMACS_RELEASE
 
-gromacs:gcc-7:test-gmxapi:
-  extends:
-    - .gromacs:base:test
-    - .gmxapi-extra-installs
-    - .use-gcc7
-  needs:
-    - job: simple-build
-      artifacts: false
-    - job: gromacs:gcc-7:build-gmxapi
-    - job: prepare-regressiontests
-  except:
-    variables:
-      - $GROMACS_RELEASE
-
-gromacs:gcc-7:release:test-gmxapi:
-  extends:
-    - .gromacs:base:test
-    - .gmxapi-extra-installs
-    - .use-gcc7
-  stage: release-tests
-  variables:
-    BUILD_DIR: release-builds-gcc
-  needs:
-    - job: gromacs:gcc-7:release:configure-gmxapi
-      artifacts: true
-    - job: gromacs:gcc-7:release:build-gmxapi
-      artifacts: true
-  only:
-    refs:
-      - triggers
-      - web
-      - schedules
-    variables:
-      - $GROMACS_RELEASE
-
 gromacs:gcc-8:test:
   extends:
     - .gromacs:base:test
@@ -1023,6 +854,8 @@ gromacs:gcc-8-cuda-10.2:test:
     REGRESSIONTEST_PME_RANK_NUMBER: 0
     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
     REGRESSIONTEST_OMP_RANK_NUMBER: 1
+    CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
+  # TODO: Enable GMX_PYTHON_PACKAGE when dependencies are in Docker image.
   extends:
     - .gromacs:base:test
     - .use-cuda
@@ -1084,41 +917,6 @@ gromacs:clang-7:release:test:
     variables:
       - $GROMACS_RELEASE
 
-gromacs:clang-7:test-gmxapi:
-  extends:
-    - .gromacs:base:test
-    - .gmxapi-extra-installs
-    - .use-clang7
-  needs:
-    - job: simple-build
-      artifacts: false
-    - job: gromacs:clang-7:build-gmxapi
-    - job: prepare-regressiontests
-  except:
-    variables:
-      - $GROMACS_RELEASE
-
-gromacs:clang-7:release:test-gmxapi:
-  extends:
-    - .gromacs:base:test
-    - .gmxapi-extra-installs
-    - .use-clang7
-  stage: release-tests
-  variables:
-    BUILD_DIR: release-builds-clang
-  needs:
-    - job: gromacs:clang-7:release:configure-gmxapi
-      artifacts: true
-    - job: gromacs:clang-7:release:build-gmxapi
-      artifacts: true
-  only:
-    refs:
-      - triggers
-      - web
-      - schedules
-    variables:
-      - $GROMACS_RELEASE
-
 gromacs:clang-8:test:
   extends:
     - .gromacs:base:test

diff --git a/admin/gitlab-ci/lint.gitlab-ci.yml b/admin/gitlab-ci/lint.gitlab-ci.yml
index 361d97c9f828bad5e4f0c75b3358a0277dc36358..9ac85814bff67460ecdb04ff8be8c85570f5f2bc 100644 (file)
--- a/admin/gitlab-ci/lint.gitlab-ci.yml
+++ b/admin/gitlab-ci/lint.gitlab-ci.yml
@@ -11,6 +11,8 @@ configure-clang-tidy:
     BUILD_DIR: build-clang-tidy
     CMAKE_EXTRA_OPTIONS: -DCLANG_TIDY=clang-tidy-$COMPILER_MAJOR_VERSION -DGMX_CLANG_TIDY=ON -DGMX_COMPILER_WARNINGS=ON
     EXTRA_INSTALLS: clang-tidy-$COMPILER_MAJOR_VERSION
+    CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
+  # TODO: Enable GMX_PYTHON_PACKAGE for clang-tidy when dependencies are in Docker image.
   except:
     variables:
       - $GROMACS_RELEASE
@@ -136,7 +138,7 @@ linkchecker:
     - .build-docs-webpage
   stage: nightly-build
   dependencies:
-    - webpage-gmxapi
+    - webpage
   only:
     - web
     - schedules
@@ -149,7 +151,7 @@ linkchecker:
     KUBERNETES_CPU_LIMIT: 1
     KUBERNETES_CPU_REQUEST: 1
     KUBERNETES_MEMORY_LIMIT: 2Gi
-    BUILD_DIR: build-docs-gmxapi
+    BUILD_DIR: build-docs
   script:
     - cd $BUILD_DIR
     - linkchecker docs/html/index.html -f ../docs/linkcheckerrc -Fxml --ignore-url html-full