From 45e835f1972b5b2c34265b71c6eec5424606db6b Mon Sep 17 00:00:00 2001
From: ProfOak <OpenProfOak@gmail.com>
Date: Mon, 5 Jun 2023 15:39:21 -0500
Subject: [PATCH 01/10] DEV-1834: Don't do anything with gdcdatamodel2

---
 .gitlab-ci.yml | 112 -------------------------------------------------
 1 file changed, 112 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5a7e8fbdf..76dac8a29 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,8 +4,6 @@
 
 stages:
   - test
-  - build
-  - release_gdcdatamodel2
 
 include:
   - project: nci-gdc/gitlab-templates
@@ -53,113 +51,3 @@ release:
     - when: always
       variables:
         GDCDICTIONARY_TARGET_VERSION: $CI_COMMIT_REF_NAME
-
-update_reqs_for_gdcdatamodel2:
-  image: docker.osdc.io/ncigdc/python36-builder:1.4.0
-  stage: build
-  script:
-    - !reference [.load_github_key, script]
-    - git clone git@github.com:NCI-GDC/gdcdatamodel2.git
-    - cd gdcdatamodel2
-    - git checkout "$GDCDICTIONARY_TARGET_VERSION" || git checkout -b "$GDCDICTIONARY_TARGET_VERSION"
-    - git log -1
-    - sed -i 's|gdcdictionary @ git+https://github.com/NCI-GDC/gdcdictionary.git@.*#egg=gdcdictionary|gdcdictionary @ git+https://github.com/NCI-GDC/gdcdictionary.git@'"$GDCDICTIONARY_TARGET_VERSION"'#egg=gdcdictionary|' setup.cfg
-    - cat setup.cfg
-    - pip3 --version
-    - pip3 install virtualenv pip-tools==6.3.0
-    - pip-compile -i https://pypi.org/simple --extra=dev --output-file=dev-requirements.txt pyproject.toml
-  artifacts:
-    paths:
-      - gdcdatamodel2/setup.cfg
-      - gdcdatamodel2/dev-requirements.txt
-    expire_in: 1 week
-  rules:
-    - !reference [.override_gdcdictionary_version, rules]
-
-
-
-execute_plaster:
-  image: docker.osdc.io/ncigdc/python3.8-builder:2.1.0
-  stage: build
-  script:
-    - !reference [.load_github_key, script]
-    - pwd
-    - git clone git@github.com:NCI-GDC/gdcdatamodel2.git
-    - cd gdcdatamodel2
-    - git checkout "$GDCDICTIONARY_TARGET_VERSION" || git checkout -b "$GDCDICTIONARY_TARGET_VERSION"
-    - git log -1
-    - sed -i 's|version = .*|version ="'"$GDCDICTIONARY_TARGET_VERSION"'"|' plaster.toml
-    - sed -i 's/is_git_tag = .*/is_git_tag = false/' plaster.toml
-    - cat plaster.toml
-    - bash plaster
-    - git status
-    - rm setup.cfg dev-requirements.txt
-  artifacts:
-    paths:
-      - gdcdatamodel2
-    expire_in: 1 week
-  rules:
-    - !reference [.override_gdcdictionary_version, rules]
-
-
-release_datamodels_to_nexus:
-  image: docker.osdc.io/ncigdc/python36-builder:1.4.0
-  stage: release_gdcdatamodel2
-  script:
-    - cd gdcdatamodel2
-    - ls -R .
-    - cat setup.cfg
-    - cat dev-requirements.txt
-    - whoami
-    - apt-get update
-    - apt-get install -y python3-venv
-    - pip3 install -U setuptools_scm build twine setuptools
-    - python3 -m setuptools_scm
-    - python3 -m build
-    - twine check dist/*
-    - twine upload dist/*
-  variables:
-    TWINE_USERNAME: ${TWINE_USER}
-    TWINE_PASSWORD: ${TWINE_PASSWORD}
-  artifacts:
-    paths:
-      - dist/*.whl
-    reports:
-      dotenv: vars.env
-  rules: # Override globally-defined RELEASE_REGISTRY
-    - if: $CI_COMMIT_TAG
-      when: always
-      variables:
-        TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
-    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
-      when: always
-      variables:
-        TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
-    - if: $CI_COMMIT_REF_NAME =~ /master/
-      when: always
-      variables:
-        TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
-    - if: $CI_COMMIT_REF_NAME =~ /main/
-      when: always
-      variables:
-        TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
-    - when: always
-  needs: ['update_reqs_for_gdcdatamodel2', 'execute_plaster']
-
-
-push_datamodels_to_github:
-  image: docker.osdc.io/ncigdc/python36-builder:1.4.0
-  stage: release_gdcdatamodel2
-  script:
-    - !reference [.load_github_key, script]
-    - cd gdcdatamodel2
-    - cat setup.cfg
-    - cat dev-requirements.txt
-    - git status
-    - git add .
-    - git commit -m "Use gdcdictionary $GDCDICTIONARY_TARGET_VERSION $CI_COMMIT_SHA"
-    - git push origin "$GDCDICTIONARY_TARGET_VERSION"
-  allow_failure: true   # failure when no changes of models
-  rules:
-    - !reference [.override_gdcdictionary_version, rules]
-  needs: ['update_reqs_for_gdcdatamodel2', 'execute_plaster']

From 027aefd49d39c333480249f173a8c2ca0ec98040 Mon Sep 17 00:00:00 2001
From: ProfOak <OpenProfOak@gmail.com>
Date: Mon, 5 Jun 2023 17:13:10 -0500
Subject: [PATCH 02/10] DEV-1834: add more python versions

---
 .gitlab-ci.yml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 76dac8a29..5aecccc06 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -22,15 +22,10 @@ variables:
   TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-snapshots/"
 
 
-tox:
-  image: ${BASE_CONTAINER_REGISTRY}/${REPO_PY_VERSION}-builder:${BASE_CONTAINER_VERSION}
-  before_script:
-    - mkdir -p /usr/share/man/man1
-
 .python_versions:
   parallel:
     matrix:
-      - REPO_PY_VERSION: ["python36"]
+      - REPO_PY_VERSION: ["python36", "python37", "python38", "python39"]
 
 docker_build:
   allow_failure: true

From a7d4f159ba7b834a0a9cfbd51d43b3e365751eac Mon Sep 17 00:00:00 2001
From: Arthur Collet <acollet@uchicago.edu>
Date: Tue, 6 Jun 2023 13:22:44 -0500
Subject: [PATCH 03/10] Using 0.2.0 of gitlab-templates

---
 .gitlab-ci.yml | 39 ++++++++++++++++-----------------------
 1 file changed, 16 insertions(+), 23 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5aecccc06..fdbad82c2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -7,36 +7,29 @@ stages:
 
 include:
   - project: nci-gdc/gitlab-templates
-    ref: master
+    ref: 0.2.0
     file:
       - templates/global/full.yaml
       - templates/python/full.yaml
 
-variables:
-  BASE_CONTAINER_VERSION: "1.4.0"
-  PRE_COMMIT_DOCKER_IMAGE: docker.osdc.io/ncigdc/python3.7-builder:2.2.0
-  DOCKER_BUILDKIT: 1
-  PIP_EXTRA_INDEX_URL: https://nexus.osdc.io/repository/pypi-all/simple
-  DOCKER_BUILD_OPTS: "--build-arg PIP_EXTRA_INDEX_URL=https://nexus.osdc.io/repository/pypi-all/simple"
-  DOCKER_PUSH_OPTS: "--all-tags"
-  TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-snapshots/"
-
-
 .python_versions:
   parallel:
     matrix:
-      - REPO_PY_VERSION: ["python36", "python37", "python38", "python39"]
-
-docker_build:
-  allow_failure: true
-  rules:
-    - when: never
-
-release:
-  image: docker.osdc.io/ncigdc/python36-builder:1.4.0
-  allow_failure: true
-  rules:
-    - when: never
+      - REPO_PY_VERSION: ["python3.7", "python3.8", "python3.9"]
+
+tox:
+  stage: test
+  image: ${BASE_CONTAINER_REGISTRY}/${REPO_PY_VERSION}-builder:${BASE_CONTAINER_VERSION}
+  script:
+    - pip install tox
+    - tox
+
+tox legacy:
+  stage: test
+  image: ${BASE_CONTAINER_REGISTRY}/python36-builder:${LEGACY_BASE_CONTAINER_VERSION}
+  script:
+    - pip install tox
+    - tox -e py36
 
 .override_gdcdictionary_version:
   rules:

From 7048e5ab4ed91a40deec2edb2fe17e08fdec7d7c Mon Sep 17 00:00:00 2001
From: Arthur Collet <acollet@uchicago.edu>
Date: Tue, 6 Jun 2023 13:28:25 -0500
Subject: [PATCH 04/10] Using 0.2.0 of gitlab-templates

---
 .gitlab-ci.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index fdbad82c2..e64fee78f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -12,14 +12,12 @@ include:
       - templates/global/full.yaml
       - templates/python/full.yaml
 
-.python_versions:
-  parallel:
-    matrix:
-      - REPO_PY_VERSION: ["python3.7", "python3.8", "python3.9"]
-
 tox:
   stage: test
   image: ${BASE_CONTAINER_REGISTRY}/${REPO_PY_VERSION}-builder:${BASE_CONTAINER_VERSION}
+  parallel:
+    matrix:
+      - REPO_PY_VERSION: ["python3.7", "python3.8", "python3.9"]
   script:
     - pip install tox
     - tox

From 7b8e9916043ac61e604f6e08d7b54f551a8c5955 Mon Sep 17 00:00:00 2001
From: Arthur Collet <acollet@uchicago.edu>
Date: Tue, 6 Jun 2023 13:34:01 -0500
Subject: [PATCH 05/10] Specify tox environment

---
 .gitlab-ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e64fee78f..af33586da 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -14,13 +14,13 @@ include:
 
 tox:
   stage: test
-  image: ${BASE_CONTAINER_REGISTRY}/${REPO_PY_VERSION}-builder:${BASE_CONTAINER_VERSION}
+  image: ${BASE_CONTAINER_REGISTRY}/python${REPO_PY_VERSION}-builder:${BASE_CONTAINER_VERSION}
   parallel:
     matrix:
-      - REPO_PY_VERSION: ["python3.7", "python3.8", "python3.9"]
+      - REPO_PY_VERSION: ["3.7", "3.8", "3.9"]
   script:
     - pip install tox
-    - tox
+    - tox -e ${REPO_PY_VERSION}
 
 tox legacy:
   stage: test

From 1212534991bd4dea2189262277140c9cb52c4aac Mon Sep 17 00:00:00 2001
From: ProfOak <OpenProfOak@gmail.com>
Date: Wed, 7 Jun 2023 17:33:14 -0500
Subject: [PATCH 06/10] DEV-1834: add extra rule for tags

... and re-add stages removed in earlier commit
---
 .gitlab-ci.yml | 113 ++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 111 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index af33586da..766aa46cc 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -29,11 +29,120 @@ tox legacy:
     - pip install tox
     - tox -e py36
 
+# These rules determine when the plaster steps execute.
 .override_gdcdictionary_version:
   rules:
     - if: $GDCDICTIONARY_TARGET_VERSION_OVERRIDE != null
       variables:
         GDCDICTIONARY_TARGET_VERSION: $GDCDICTIONARY_TARGET_VERSION_OVERRIDE
-    - when: always
+    - if: $CI_COMMIT_TAG != null
       variables:
-        GDCDICTIONARY_TARGET_VERSION: $CI_COMMIT_REF_NAME
+        GDCDICTIONARY_TARGET_VERSION: $CI_COMMIT_TAG
+    - if: $CI_COMMIT_REF_NAME =~ /^(master|main|release)/
+      when: never
+
+update_reqs_for_gdcdatamodel2:
+  image: docker.osdc.io/ncigdc/python36-builder:1.4.0
+  stage: build
+  script:
+    - !reference [.load_github_key, script]
+    - git clone git@github.com:NCI-GDC/gdcdatamodel2.git
+    - cd gdcdatamodel2
+    - git checkout "$GDCDICTIONARY_TARGET_VERSION" || git checkout -b "$GDCDICTIONARY_TARGET_VERSION"
+    - git log -1
+    - sed -i 's|gdcdictionary @ git+https://github.com/NCI-GDC/gdcdictionary.git@.*#egg=gdcdictionary|gdcdictionary @ git+https://github.com/NCI-GDC/gdcdictionary.git@'"$GDCDICTIONARY_TARGET_VERSION"'#egg=gdcdictionary|' setup.cfg
+    - cat setup.cfg
+    - pip3 --version
+    - pip3 install virtualenv pip-tools==6.3.0
+    - pip-compile -i https://pypi.org/simple --extra=dev --output-file=dev-requirements.txt pyproject.toml
+  artifacts:
+    paths:
+      - gdcdatamodel2/setup.cfg
+      - gdcdatamodel2/dev-requirements.txt
+    expire_in: 1 week
+  rules:
+    - !reference [.override_gdcdictionary_version, rules]
+
+execute_plaster:
+  image: docker.osdc.io/ncigdc/python3.8-builder:2.1.0
+  stage: build
+  script:
+    - !reference [.load_github_key, script]
+    - pwd
+    - git clone git@github.com:NCI-GDC/gdcdatamodel2.git
+    - cd gdcdatamodel2
+    - git checkout "$GDCDICTIONARY_TARGET_VERSION" || git checkout -b "$GDCDICTIONARY_TARGET_VERSION"
+    - git log -1
+    - sed -i 's|version = .*|version ="'"$GDCDICTIONARY_TARGET_VERSION"'"|' plaster.toml
+    - sed -i 's/is_git_tag = .*/is_git_tag = false/' plaster.toml
+    - cat plaster.toml
+    - bash plaster
+    - git status
+    - rm setup.cfg dev-requirements.txt
+  artifacts:
+    paths:
+      - gdcdatamodel2
+    expire_in: 1 week
+  rules:
+    - !reference [.override_gdcdictionary_version, rules]
+
+release_datamodels_to_nexus:
+  image: docker.osdc.io/ncigdc/python36-builder:1.4.0
+  stage: release_gdcdatamodel2
+  script:
+    - cd gdcdatamodel2
+    - ls -R .
+    - cat setup.cfg
+    - cat dev-requirements.txt
+    - whoami
+    - apt-get update
+    - apt-get install -y python3-venv
+    - pip3 install -U setuptools_scm build twine setuptools
+    - python3 -m setuptools_scm
+    - python3 -m build
+    - twine check dist/*
+    - twine upload dist/*
+  variables:
+    TWINE_USERNAME: ${TWINE_USER}
+    TWINE_PASSWORD: ${TWINE_PASSWORD}
+  artifacts:
+    paths:
+      - dist/*.whl
+    reports:
+      dotenv: vars.env
+  rules: # Override globally-defined RELEASE_REGISTRY
+    - if: $CI_COMMIT_TAG
+      when: always
+      variables:
+        TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
+    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
+      when: always
+      variables:
+        TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
+    - if: $CI_COMMIT_REF_NAME =~ /master/
+      when: always
+      variables:
+        TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
+    - if: $CI_COMMIT_REF_NAME =~ /main/
+      when: always
+      variables:
+        TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
+    - when: always
+  needs: ['update_reqs_for_gdcdatamodel2', 'execute_plaster']
+
+push_datamodels_to_github:
+  image: docker.osdc.io/ncigdc/python36-builder:1.4.0
+  stage: release_gdcdatamodel2
+  script:
+    - !reference [.load_github_key, script]
+    - cd gdcdatamodel2
+    - cat setup.cfg
+    - cat dev-requirements.txt
+    - git status
+    - git add .
+    - git commit -m "Use gdcdictionary $GDCDICTIONARY_TARGET_VERSION $CI_COMMIT_SHA"
+    - git push origin "$GDCDICTIONARY_TARGET_VERSION"
+  allow_failure: true   # failure when no changes of models
+  rules:
+    - !reference [.override_gdcdictionary_version, rules]
+  needs: ['update_reqs_for_gdcdatamodel2', 'execute_plaster']

From 8f87d9756bce20abebb57ce571f8105476b98bd4 Mon Sep 17 00:00:00 2001
From: ProfOak <OpenProfOak@gmail.com>
Date: Thu, 8 Jun 2023 12:30:33 -0500
Subject: [PATCH 07/10] DEV-1834: add back missing stages

---
 .gitlab-ci.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 766aa46cc..3f71bea0f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,6 +4,8 @@
 
 stages:
   - test
+  - build
+  - release_gdcdatamodel2
 
 include:
   - project: nci-gdc/gitlab-templates

From 856547700d49d5dc45111c894fb31225eafc9527 Mon Sep 17 00:00:00 2001
From: ProfOak <OpenProfOak@gmail.com>
Date: Thu, 8 Jun 2023 13:07:08 -0500
Subject: [PATCH 08/10] DEV-1834: Replace needs with dependencies

The needs keyword is for out-of-order build stages. We keep the
processes in order but we only want the full sequence to go if the rules
are met for the first build step.
---
 .gitlab-ci.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3f71bea0f..c56e9161a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -130,7 +130,9 @@ release_datamodels_to_nexus:
       variables:
         TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
     - when: always
-  needs: ['update_reqs_for_gdcdatamodel2', 'execute_plaster']
+  dependencies:
+    - update_reqs_for_gdcdatamodel2
+    - execute_plaster
 
 push_datamodels_to_github:
   image: docker.osdc.io/ncigdc/python36-builder:1.4.0
@@ -147,4 +149,6 @@ push_datamodels_to_github:
   allow_failure: true   # failure when no changes of models
   rules:
     - !reference [.override_gdcdictionary_version, rules]
-  needs: ['update_reqs_for_gdcdatamodel2', 'execute_plaster']
+  dependencies:
+    - update_reqs_for_gdcdatamodel2
+    - execute_plaster

From fcd124ab8272045dc5eda88a52c5a7517d20523e Mon Sep 17 00:00:00 2001
From: ProfOak <OpenProfOak@gmail.com>
Date: Thu, 8 Jun 2023 14:28:26 -0500
Subject: [PATCH 09/10] DEV-1834: Change rules block on final build step

---
 .gitlab-ci.yml | 20 ++------------------
 1 file changed, 2 insertions(+), 18 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c56e9161a..b2c115b82 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -112,24 +112,8 @@ release_datamodels_to_nexus:
       - dist/*.whl
     reports:
       dotenv: vars.env
-  rules: # Override globally-defined RELEASE_REGISTRY
-    - if: $CI_COMMIT_TAG
-      when: always
-      variables:
-        TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
-    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
-      when: always
-      variables:
-        TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
-    - if: $CI_COMMIT_REF_NAME =~ /master/
-      when: always
-      variables:
-        TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
-    - if: $CI_COMMIT_REF_NAME =~ /main/
-      when: always
-      variables:
-        TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-releases/"
-    - when: always
+  rules:
+    - !reference [.override_gdcdictionary_version, rules]
   dependencies:
     - update_reqs_for_gdcdatamodel2
     - execute_plaster

From f72d3e4770a1affefebc0c51d073a40531c090fc Mon Sep 17 00:00:00 2001
From: ProfOak <OpenProfOak@gmail.com>
Date: Tue, 11 Jul 2023 15:30:04 -0500
Subject: [PATCH 10/10] DEV-1834: re-remove variables

They get pulled from the gitlab templates repo.
---
 .gitlab-ci.yml | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 334913a1d..b2c115b82 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -14,15 +14,6 @@ include:
       - templates/global/full.yaml
       - templates/python/full.yaml
 
-variables:
-  BASE_CONTAINER_VERSION: "1.4.0"
-  PRE_COMMIT_DOCKER_IMAGE: docker.osdc.io/ncigdc/python3.7-builder:2.2.0
-  DOCKER_BUILDKIT: 1
-  PIP_EXTRA_INDEX_URL: https://nexus.osdc.io/repository/pypi-all/simple
-  DOCKER_BUILD_OPTS: "--build-arg PIP_EXTRA_INDEX_URL=https://nexus.osdc.io/repository/pypi-all/simple"
-  DOCKER_PUSH_OPTS: "--all-tags"
-  TWINE_REPOSITORY_URL: "https://nexus.osdc.io/repository/pypi-snapshots/"
-
 tox:
   stage: test
   image: ${BASE_CONTAINER_REGISTRY}/python${REPO_PY_VERSION}-builder:${BASE_CONTAINER_VERSION}