DEV 2005 add gitlab ci (#409)

* add gitlab ci * update deps * remove requiremtns.txt in tox * get db var from env * format setup.py --------- Co-authored-by: Arthur Collet <acollet@uchicago.edu>
NCI-GDC · Jul 21, 2023 · ae5dd8e · ae5dd8e
1 parent e843b7f
commit ae5dd8e
Show file tree

Hide file tree

Showing 12 changed files with 164 additions and 242 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -0,0 +1,46 @@
+---
+
+include:
+  - project: nci-gdc/gitlab-templates
+    ref: 0.2.1
+    file:
+      - templates/global/full.yaml
+      - templates/python/full.yaml
+      - templates/common/python.yaml
+
+tox:
+  stage: test
+  parallel:
+    matrix:
+      - PYTHON_VERSION: ['3.6', '3.7', '3.8']
+  image: ${BASE_CONTAINER_REGISTRY}/python${PYTHON_VERSION}-builder:${BASE_CONTAINER_VERSION}
+  services:
+    - name: docker.osdc.io/ncigdc/ci-postgres-13:feat_dev-1924-postgres-init-script-3673ef90
+      alias: postgres
+  tags:
+    - dind
+  variables:
+    # these are for postgres docker
+    POSTGRES_HOST_AUTH_METHOD: trust
+    PG_HOST: postgres
+    PG_INIT_SQL: |
+      create user test with superuser password 'test';
+      create database automated_test with owner test;
+      create database dev_models with owner test;
+  before_script:
+    - !reference [.load_github_key, script]
+    - pip install "tox<4"
+  script:
+    - tox -r -e py
+
+
+# used by release
+.python_versions:
+  parallel:
+    matrix:
+      - BUILD_PY_VERSION: [python3.6]
+      - RELEASE_PY_VERSION: [python3.6]
+
+release:
+  before_script:
+    - git fetch --unshallow || true
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -3,7 +3,7 @@
     "files": "^.secrets.baseline$",
     "lines": null
   },
-  "generated_at": "2022-10-14T21:28:31Z",
+  "generated_at": "2023-07-21T18:27:05Z",
   "plugins_used": [
     {
       "name": "AWSKeyDetector"
@@ -60,7 +60,7 @@
         "hashed_secret": "5d0fa74acf95d1d6bebd0d37f76a94e77d604fd9",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 41,
+        "line_number": 35,
         "type": "Basic Auth Credentials"
       }
     ],
@@ -69,7 +69,7 @@
         "hashed_secret": "5d0fa74acf95d1d6bebd0d37f76a94e77d604fd9",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 36,
+        "line_number": 38,
         "type": "Basic Auth Credentials"
       }
     ]

diff --git a/dev-requirements.in b/dev-requirements.in
diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -2,246 +2,88 @@
 # This file is autogenerated by pip-compile with python 3.6
 # To update, run:
 #
-#    pip-compile --output-file=dev-requirements.txt dev-requirements.in
+#    pip-compile --extra=dev --output-file=dev-requirements.txt
 #
-argon2-cffi==21.3.0
-    # via notebook
-argon2-cffi-bindings==21.2.0
-    # via argon2-cffi
-async-generator==1.10
-    # via nbclient
 attrs==22.2.0
     # via
-    #   -c requirements.txt
+    #   gdcdictionary
     #   jsonschema
     #   pytest
-backcall==0.2.0
-    # via ipython
-bleach==4.1.0
-    # via nbconvert
 cffi==1.15.1
-    # via
-    #   -c requirements.txt
-    #   argon2-cffi-bindings
+    # via cryptography
 coverage[toml]==6.2
     # via pytest-cov
-dataclasses==0.8 ; python_version < "3.7"
-    # via
-    #   -r dev-requirements.in
-    #   argon2-cffi
+cryptography==3.4.8
+    # via gdc-ng-models
 decorator==5.1.1
-    # via
-    #   -c requirements.txt
-    #   ipython
-    #   traitlets
-defusedxml==0.7.1
-    # via nbconvert
-entrypoints==0.4
-    # via
-    #   jupyter-client
-    #   nbconvert
+    # via gdcdatamodel (setup.py)
+gdc-ng-models @ git+https://github.com/NCI-GDC/gdc-ng-models.git@1.6.4
+    # via gdcdatamodel (setup.py)
+gdcdictionary @ git+https://github.com/NCI-GDC/gdcdictionary.git@2.6.6
+    # via gdcdatamodel (setup.py)
+graphviz==0.19.1
+    # via gdcdatamodel (setup.py)
 importlib-metadata==4.8.3
     # via
-    #   -c requirements.txt
     #   jsonschema
     #   pluggy
     #   pytest
 iniconfig==1.1.1
     # via pytest
-ipykernel==5.5.6
-    # via
-    #   ipywidgets
-    #   jupyter
-    #   jupyter-console
-    #   notebook
-    #   qtconsole
-ipython==7.16.3
-    # via
-    #   ipykernel
-    #   ipywidgets
-    #   jupyter-console
-ipython-genutils==0.2.0
-    # via
-    #   ipykernel
-    #   ipywidgets
-    #   nbformat
-    #   notebook
-    #   qtconsole
-    #   traitlets
-ipywidgets==7.7.5
-    # via jupyter
-jedi==0.17.2
-    # via ipython
-jinja2==3.0.3
-    # via
-    #   nbconvert
-    #   notebook
 jsonschema==3.2.0
     # via
-    #   -c requirements.txt
-    #   nbformat
-jupyter==1.0.0
-    # via -r dev-requirements.in
-jupyter-client==7.1.2
-    # via
-    #   -r dev-requirements.in
-    #   ipykernel
-    #   jupyter-console
-    #   nbclient
-    #   notebook
-    #   qtconsole
-jupyter-console==6.4.3
-    # via
-    #   -r dev-requirements.in
-    #   jupyter
-jupyter-core==4.9.2
-    # via
-    #   -r dev-requirements.in
-    #   jupyter-client
-    #   nbconvert
-    #   nbformat
-    #   notebook
-    #   qtconsole
-jupyterlab-pygments==0.1.2
-    # via nbconvert
-jupyterlab-widgets==1.1.4
-    # via ipywidgets
-markupsafe==2.0.1
-    # via jinja2
-mistune==0.8.4
-    # via nbconvert
-nbclient==0.5.9
-    # via nbconvert
-nbconvert==6.0.7
-    # via
-    #   jupyter
-    #   notebook
-nbformat==5.1.3
-    # via
-    #   nbclient
-    #   nbconvert
-    #   notebook
-nest-asyncio==1.5.6
-    # via
-    #   jupyter-client
-    #   nbclient
-    #   notebook
-notebook==6.4.10
-    # via
-    #   -r dev-requirements.in
-    #   jupyter
-    #   widgetsnbextension
+    #   gdcdatamodel (setup.py)
+    #   gdcdictionary
 packaging==21.3
-    # via
-    #   bleach
-    #   pytest
-    #   qtpy
-pandocfilters==1.5.0
-    # via nbconvert
-parso==0.7.1
-    # via jedi
-pexpect==4.8.0
-    # via ipython
-pickleshare==0.7.5
-    # via ipython
+    # via pytest
 pluggy==1.0.0
     # via pytest
-prometheus-client==0.16.0
-    # via notebook
-prompt-toolkit==3.0.36
+psqlgraph @ git+https://github.com/NCI-GDC/psqlgraph.git@4.0.1
+    # via gdcdatamodel (setup.py)
+psycopg2==2.9.6
     # via
-    #   ipython
-    #   jupyter-console
-ptyprocess==0.7.0
-    # via
-    #   pexpect
-    #   terminado
+    #   gdc-ng-models
+    #   psqlgraph
 py==1.11.0
     # via pytest
 pycparser==2.21
-    # via
-    #   -c requirements.txt
-    #   cffi
-pygments==2.14.0
-    # via
-    #   ipython
-    #   jupyter-console
-    #   jupyterlab-pygments
-    #   nbconvert
-    #   qtconsole
+    # via cffi
 pyparsing==3.0.9
     # via packaging
 pyrsistent==0.18.0
     # via
-    #   -c requirements.txt
+    #   gdcdatamodel (setup.py)
     #   jsonschema
 pytest==7.0.1
     # via
-    #   -r dev-requirements.in
+    #   gdcdatamodel (setup.py)
     #   pytest-cov
 pytest-cov==4.0.0
-    # via -r dev-requirements.in
-python-dateutil==2.8.2
-    # via jupyter-client
-pyzmq==25.0.2
-    # via
-    #   jupyter-client
-    #   notebook
-    #   qtconsole
-qtconsole==5.2.2
-    # via jupyter
-qtpy==2.0.1
-    # via qtconsole
-send2trash==1.8.2
-    # via notebook
+    # via gdcdatamodel (setup.py)
+pytz==2020.5
+    # via
+    #   gdc-ng-models
+    #   gdcdatamodel (setup.py)
+pyyaml==6.0.1
+    # via gdcdictionary
+rstr==3.0.0
+    # via psqlgraph
 six==1.16.0
+    # via jsonschema
+sqlalchemy==1.3.24
     # via
-    #   -c requirements.txt
-    #   bleach
-    #   jsonschema
-    #   python-dateutil
-    #   traitlets
-terminado==0.12.1
-    # via notebook
-testpath==0.6.0
-    # via nbconvert
+    #   gdc-ng-models
+    #   psqlgraph
 tomli==1.2.3
     # via
     #   coverage
     #   pytest
-tornado==6.1
-    # via
-    #   ipykernel
-    #   jupyter-client
-    #   notebook
-    #   terminado
-traitlets==4.3.3
-    # via
-    #   ipykernel
-    #   ipython
-    #   ipywidgets
-    #   jupyter-client
-    #   jupyter-core
-    #   nbclient
-    #   nbconvert
-    #   nbformat
-    #   notebook
-    #   qtconsole
 typing-extensions==4.1.1
-    # via
-    #   -c requirements.txt
-    #   argon2-cffi
-    #   importlib-metadata
-wcwidth==0.2.6
-    # via prompt-toolkit
-webencodings==0.5.1
-    # via bleach
-widgetsnbextension==3.6.4
-    # via ipywidgets
+    # via importlib-metadata
+xlocal==0.5
+    # via psqlgraph
 zipp==3.6.0
-    # via
-    #   -c requirements.txt
-    #   importlib-metadata
+    # via importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file:
 # setuptools
diff --git a/setup.py b/setup.py
@@ -18,6 +18,19 @@
         "gdc-ng-models @ git+https://github.com/NCI-GDC/gdc-ng-models.git@1.6.4#egg=gdc-ng-models",
         "psqlgraph @ git+https://github.com/NCI-GDC/psqlgraph.git@4.0.1#egg=psqlgraph",
     ],
+    extras_require={
+        "dev": [
+            "pytest",
+            "pytest-cov",
+        ],
+        "jupyter": [
+            "notebook",
+            "jupyter",
+            "jupyter-client",
+            "jupyter-console",
+            "jupyter-core"
+        ]
+    },
     package_data={
         "gdcdatamodel": [
             "xml_mappings/*.yaml",