Merge master into develop post Elion release

.gitignore

@@ -8,6 +8,7 @@ __pycache__/
 # Distribution / packaging
 .Python
 env/
+.venv
 venv
 venv*/
 build/

.pre-commit-config.yaml

@@ -1,51 +1,7 @@
 ---
 repos:
-  - repo: git@github.com:Yelp/detect-secrets
+-   repo: git@github.com:Yelp/detect-secrets
     rev: v0.13.0
     hooks:
-      - id: detect-secrets
-        args: [--baseline, .secrets.baseline]
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0 # last version to support py36
-    hooks:
-      - id: check-json
-      - id: check-toml
-      - id: check-yaml
-      - id: end-of-file-fixer
-      - id: fix-encoding-pragma
-        args: [--remove]
-      - id: no-commit-to-branch
-        args: [--branch, develop, --branch, master, --pattern, release/.*]
-      - id: pretty-format-json
-        args: [--autofix]
-      - id: trailing-whitespace
-        args: [--markdown-linebreak-ext=md]
-  - repo: https://github.com/psf/black
-    rev: 20.8b1  # for pre-commit 1.21.0 in jenkins
-    hooks:
-      - id: black
-        additional_dependencies: [click==8.0.4]
-  - repo: https://github.com/pycqa/isort
-    rev: 5.6.4    # last version to support pre-commit 1.21.0 in Jenkins
-    hooks:
-      - id: isort
-        name: isort (python)
-        args: [--profile, black]
-      - id: isort
-        name: isort (cython)
-        types: [cython]
-        args: [--profile, black]
-      - id: isort
-        name: isort (pyi)
-        types: [pyi]
-        args: [--profile, black]
-  - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
-    rev: 0.2.1
-    hooks:
-      - id: yamlfmt
-        args: [--mapping, '2', --sequence, '4', --offset, '2', --width, '80']
-  - repo: https://github.com/pappasam/toml-sort
-    rev: v0.19.0 # last version to support py36
-    hooks:
-      - id: toml-sort
-        args: [--in-place]
+    -   id: detect-secrets
+        args: ['--baseline', '.secrets.baseline']

dev-requirements.txt

@@ -4,18 +4,17 @@
 #
 #    pip-compile dev-requirements.in
 #
-
 aspy.yaml==1.3.0
     # via pre-commit
-atomicwrites==1.4.0
+atomicwrites==1.4.1
     # via pytest
-attrs==21.2.0
+attrs==22.1.0
     # via
     #   -c requirements.txt
     #   jsonschema
     #   pytest
-backports.entry-points-selectable==1.1.0
-    # via virtualenv
+backcall==0.2.0
+    # via ipython
 bleach==3.3.1
     # via nbconvert
 cfgv==2.0.1
@@ -29,18 +28,17 @@ decorator==4.4.2
     #   traitlets
 defusedxml==0.7.1
     # via nbconvert
-distlib==0.3.2
+distlib==0.3.6
     # via virtualenv
 entrypoints==0.3
     # via nbconvert
-filelock==3.0.12
+filelock==3.2.1
     # via virtualenv
 identify==1.6.2
     # via pre-commit
-importlib-metadata==2.1.1
+importlib-metadata==2.1.3
     # via
     #   -c requirements.txt
-    #   backports.entry-points-selectable
     #   jsonschema
     #   pluggy
     #   pre-commit
@@ -50,7 +48,7 @@ importlib-resources==3.2.1
     # via
     #   pre-commit
     #   virtualenv
-ipykernel==4.10.1
+ipykernel==5.5.6
     # via
     #   ipywidgets
     #   jupyter
@@ -59,17 +57,21 @@ ipykernel==4.10.1
     #   qtconsole
 ipython-genutils==0.2.0
     # via
+    #   ipykernel
+    #   ipywidgets
     #   nbformat
     #   notebook
     #   qtconsole
     #   traitlets
-ipython==5.10.0
+ipython==7.9.0
     # via
     #   ipykernel
     #   ipywidgets
     #   jupyter-console
-ipywidgets==7.6.3
+ipywidgets==7.7.2
     # via jupyter
+jedi==0.17.2
+    # via ipython
 jinja2==2.11.3
     # via
     #   nbconvert
@@ -103,15 +105,14 @@ markupsafe==1.1.1
     # via jinja2
 mistune==0.8.4
     # via nbconvert
-more-itertools==5.0.0
+more-itertools==8.14.0
     # via pytest
 nbconvert==5.6.1
     # via
     #   jupyter
     #   notebook
-nbformat==4.4.0
+nbformat==5.1.3
     # via
-    #   ipywidgets
     #   nbconvert
     #   notebook
 nodeenv==1.6.0
@@ -125,8 +126,10 @@ packaging==20.9
     # via
     #   bleach
     #   pytest
-pandocfilters==1.4.3
+pandocfilters==1.5.0
     # via nbconvert
+parso==0.7.1
+    # via jedi
 pathlib2==2.3.7.post1
     # via pytest
 pexpect==4.8.0
@@ -139,15 +142,15 @@ pluggy==0.13.1
     # via pytest
 pre-commit==1.21.0
     # via -r dev-requirements.in
-prompt-toolkit==1.0.18
+prompt-toolkit==2.0.10
     # via ipython
 ptyprocess==0.7.0
     # via
     #   pexpect
     #   terminado
-py==1.10.0
+py==1.11.0
     # via pytest
-pygments==2.5.2
+pygments==2.11.2
     # via
     #   ipython
     #   nbconvert
@@ -169,23 +172,20 @@ pyyaml==5.3.1
     #   -c requirements.txt
     #   aspy.yaml
     #   pre-commit
-pyzmq==19.0.2
+pyzmq==20.0.0
     # via
     #   jupyter-client
     #   qtconsole
 qtconsole==4.7.7
     # via jupyter
 qtpy==1.9.0
     # via qtconsole
-simplegeneric==0.8.1
-    # via ipython
 six==1.15.0
     # via
     #   -c requirements.txt
     #   bleach
     #   cfgv
     #   jsonschema
-    #   more-itertools
     #   pathlib2
     #   pre-commit
     #   prompt-toolkit
@@ -194,11 +194,11 @@ six==1.15.0
     #   virtualenv
 terminado==0.8.3
     # via notebook
-testpath==0.4.4
+testpath==0.6.0
     # via nbconvert
 toml==0.10.2
     # via pre-commit
-tornado==5.1.1
+tornado==6.1
     # via
     #   ipykernel
     #   notebook
@@ -214,15 +214,15 @@ traitlets==4.3.3
     #   nbformat
     #   notebook
     #   qtconsole
-virtualenv==20.7.2
+virtualenv==20.15.1
     # via pre-commit
-wcwidth==0.2.5
+wcwidth==0.2.6
     # via
     #   prompt-toolkit
     #   pytest
 webencodings==0.5.1
     # via bleach
-widgetsnbextension==3.5.1
+widgetsnbextension==3.6.1
     # via ipywidgets
 zipp==1.2.0
     # via

requirements.txt

@@ -2,20 +2,19 @@
 # This file is autogenerated by pip-compile
 # To update, run:
 #
-#    pip-compile
+#    pip-compile setup.py
 #
-
-attrs==21.2.0
+attrs==22.1.0
     # via jsonschema
 decorator==4.4.2
     # via gdcdatamodel (setup.py)
 git+https://github.com/NCI-GDC/gdc-ng-models.git@1.5.2#egg=gdc-ng-models
     # via gdcdatamodel (setup.py)
-git+https://github.com/NCI-GDC/gdcdictionary.git@2.5.0-rc.0#egg=gdcdictionary
+git+https://github.com/NCI-GDC/gdcdictionary.git@2.6.3#egg=gdcdictionary
     # via gdcdatamodel (setup.py)
 graphviz==0.14.2
     # via gdcdatamodel (setup.py)
-importlib-metadata==2.1.1
+importlib-metadata==2.1.3
     # via jsonschema
 jsonschema==3.2.0
     # via

setup.py

@@ -14,7 +14,7 @@
         "jsonschema~=3.2",
         "pyrsistent<0.17.0",
         "decorator<=5.0.0",
-        "gdcdictionary @ git+https://github.com/NCI-GDC/gdcdictionary.git@2.5.0-rc.0#egg=gdcdictionary",
+        "gdcdictionary @ git+https://github.com/NCI-GDC/gdcdictionary.git@2.6.3#egg=gdcdictionary",
         "gdc-ng-models @ git+https://github.com/NCI-GDC/gdc-ng-models.git@1.5.2#egg=gdc-ng-models",
         "psqlgraph @ git+https://github.com/NCI-GDC/psqlgraph.git@3.4.0#egg=psqlgraph",
     ],