DEV 2863 standardize structure (#292)

* use setup.cfg

* add pyproject.toml

* move bin/gdc-client -> src/gdc_client/cli.py

* fix console_scripts

---------

Co-authored-by: Rowland Ogwara <rogwara@uchicago.edu>

Author: qqiao2024

.gitlab-ci.yml

@@ -5,6 +5,8 @@ include:
     file:
       - templates/artifacts/python-library.yaml
 
+variables:
+  LANGUAGE_VERSION: python3.8
 
 tox:
   parallel:

bin/package

@@ -73,7 +73,6 @@ cd ..
 python -m pip install --upgrade pip
 python -m pip install --no-deps -r requirements.txt
 python -m pip install --no-deps .
-python setup.py install
 
 # go back go the ./gdc_client/bin dir
 cd bin
@@ -100,7 +99,8 @@ pyinstaller \
     --noconfirm \
     --onefile \
     --copy-metadata gdc-client \
-    -c gdc-client
+    --name gdc-client \
+    -c ../src/gdc_client/cli.py
 
 echo "Testing produced binary..."
 ./dist/$BINARY_NAME --help

dev-requirements.in

@@ -2,16 +2,16 @@
 # This file is autogenerated by pip-compile with Python 3.8
 # by the following command:
 #
-#    pip-compile dev-requirements.in
+#    pip-compile --extra=dev --output-file=dev-requirements.txt
 #
 atomicwrites==1.4.1
     # via pytest
 attrs==22.1.0
     # via pytest
 aws-sam-translator==1.11.0
     # via
-    #   -r dev-requirements.in
     #   cfn-lint
+    #   gdc-client (pyproject.toml)
 aws-xray-sdk==2.11.0
     # via moto
 boto==2.49.0
@@ -27,31 +27,26 @@ botocore==1.19.63
     #   moto
     #   s3transfer
 certifi==2024.7.4
-    # via
-    #   -c requirements.txt
-    #   requests
+    # via requests
 cffi==1.15.1
-    # via
-    #   -c requirements.txt
-    #   cryptography
+    # via cryptography
 cfn-lint==0.21.6
     # via
-    #   -r dev-requirements.in
+    #   gdc-client (pyproject.toml)
     #   moto
 chardet==3.0.4
-    # via
-    #   -c requirements.txt
-    #   requests
+    # via requests
 click==8.1.7
     # via
-    #   -r dev-requirements.in
     #   flask
-coverage==5.5
+    #   gdc-client (pyproject.toml)
+coverage[toml]==7.6.0
     # via pytest-cov
 cryptography==43.0.0
     # via
-    #   -c requirements.txt
+    #   gdc-client (pyproject.toml)
     #   moto
+    #   pyopenssl
     #   python-jose
     #   sshpubkeys
 docker==4.4.4
@@ -62,18 +57,19 @@ ecdsa==0.14.1
     #   python-jose
     #   sshpubkeys
 flask==1.0.4
-    # via -r dev-requirements.in
+    # via gdc-client (pyproject.toml)
 httmock==1.3.0
-    # via -r dev-requirements.in
+    # via gdc-client (pyproject.toml)
 idna==2.8
     # via
-    #   -c requirements.txt
     #   moto
     #   requests
 importlib-metadata==7.0.1
     # via
-    #   -c requirements.txt
+    #   gdc-client (pyproject.toml)
     #   pytest
+intervaltree==3.0.2
+    # via gdc-client (pyproject.toml)
 itsdangerous==1.1.0
     # via flask
 jinja2==2.11.3
@@ -92,9 +88,11 @@ jsonpointer==2.3
     # via jsonpatch
 jsonschema==2.6.0
     # via
-    #   -c requirements.txt
     #   aws-sam-translator
     #   cfn-lint
+    #   gdc-client (pyproject.toml)
+lxml==4.4.3
+    # via gdc-client (pyproject.toml)
 markupsafe==1.1.1
     # via
     #   jinja2
@@ -106,56 +104,65 @@ more-itertools==8.14.0
     #   moto
     #   pytest
 moto==1.3.16
-    # via -r dev-requirements.in
+    # via gdc-client (pyproject.toml)
+ndg-httpsclient==0.5.1
+    # via gdc-client (pyproject.toml)
 packaging==20.9
     # via pytest
 pluggy==0.13.1
     # via pytest
+progressbar2==4.4.2
+    # via gdc-client (pyproject.toml)
 py==1.11.0
     # via pytest
 pyasn1==0.4.8
     # via
-    #   -c requirements.txt
+    #   gdc-client (pyproject.toml)
+    #   ndg-httpsclient
     #   python-jose
     #   rsa
 pycparser==2.21
+    # via cffi
+pyopenssl==24.2.1
     # via
-    #   -c requirements.txt
-    #   cffi
+    #   gdc-client (pyproject.toml)
+    #   ndg-httpsclient
 pyparsing==2.4.7
     # via packaging
 pytest==4.6.2
     # via
-    #   -r dev-requirements.in
+    #   gdc-client (pyproject.toml)
     #   pytest-cov
-pytest-cov==2.7.1
-    # via -r dev-requirements.in
+pytest-cov==5.0.0
+    # via gdc-client (pyproject.toml)
 python-dateutil==2.8.2
     # via
     #   botocore
     #   moto
 python-jose[cryptography]==3.2.0
     # via
-    #   -r dev-requirements.in
+    #   gdc-client (pyproject.toml)
     #   moto
+python-utils==3.8.2
+    # via progressbar2
 pytz==2022.7.1
     # via moto
 pyyaml==5.3.1
     # via
-    #   -c requirements.txt
     #   cfn-lint
+    #   gdc-client (pyproject.toml)
     #   moto
 requests==2.22.0
     # via
-    #   -c requirements.txt
     #   cfn-lint
     #   docker
+    #   gdc-client (pyproject.toml)
     #   httmock
     #   moto
     #   requests-mock
     #   responses
 requests-mock==1.5.2
-    # via -r dev-requirements.in
+    # via gdc-client (pyproject.toml)
 responses==0.17.0
     # via moto
 rsa==4.7.2
@@ -164,7 +171,6 @@ s3transfer==0.3.7
     # via boto3
 six==1.16.0
     # via
-    #   -c requirements.txt
     #   aws-sam-translator
     #   cfn-lint
     #   docker
@@ -177,11 +183,18 @@ six==1.16.0
     #   requests-mock
     #   responses
     #   websocket-client
+sortedcontainers==2.4.0
+    # via intervaltree
 sshpubkeys==3.3.1
     # via moto
+termcolor==1.1.0
+    # via gdc-client (pyproject.toml)
+tomli==2.0.1
+    # via coverage
+typing-extensions==4.12.2
+    # via python-utils
 urllib3==1.25.11
     # via
-    #   -c requirements.txt
     #   botocore
     #   requests
     #   responses
@@ -199,7 +212,6 @@ xmltodict==0.13.0
     # via moto
 zipp==3.17.0
     # via
-    #   -c requirements.txt
     #   importlib-metadata
     #   moto
 

dev-requirements.txt

@@ -0,0 +1,42 @@
+[build-system]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "gdc-client"
+dynamic = [
+  "version",
+  "description",
+  "readme",
+  "requires-python",
+  "license",
+  "authors",
+  "maintainers",
+  "keywords",
+  "classifiers",
+  "urls",
+  "scripts",
+  "gui-scripts",
+  "entry-points",
+  "dependencies",
+  "optional-dependencies"
+]
+
+[tool.coverage.html]
+title = "gdc-client coverage report"
+directory = "docs/htmlcov"
+show_contexts = true
+
+[tool.coverage.run]
+branch = true
+context = "unit tests"
+source = ["gdc_client"]
+
+[tool.isort]
+extend_skip = [".md", ".json"]
+known_first_party = ["gdc_client"]
+py_version = 38
+skip = [".gitignore", ".dockerignore"]
+
+[tool.setuptools_scm]
+local_scheme = "dirty-tag"

pyproject.toml

@@ -12,46 +12,46 @@ chardet==3.0.4
     # via requests
 cryptography==43.0.0
     # via
-    #   gdc_client (setup.py)
+    #   gdc-client (pyproject.toml)
     #   pyopenssl
 idna==2.8
     # via requests
 importlib-metadata==7.0.1
-    # via gdc_client (setup.py)
+    # via gdc-client (pyproject.toml)
 intervaltree==3.0.2
-    # via gdc_client (setup.py)
+    # via gdc-client (pyproject.toml)
 jsonschema==2.6.0
-    # via gdc_client (setup.py)
+    # via gdc-client (pyproject.toml)
 lxml==4.4.2
-    # via gdc_client (setup.py)
+    # via gdc-client (pyproject.toml)
 ndg-httpsclient==0.5.0
-    # via gdc_client (setup.py)
-progressbar2==3.43.1
-    # via gdc_client (setup.py)
+    # via gdc-client (pyproject.toml)
+progressbar2==3.55.0
+    # via gdc-client (pyproject.toml)
 pyasn1==0.4.8
     # via
-    #   gdc_client (setup.py)
+    #   gdc-client (pyproject.toml)
     #   ndg-httpsclient
 pycparser==2.21
     # via cffi
 pyopenssl==24.2.1
     # via
-    #   gdc_client (setup.py)
+    #   gdc-client (pyproject.toml)
     #   ndg-httpsclient
 python-utils==2.7.1
     # via progressbar2
 pyyaml==5.3.1
-    # via gdc_client (setup.py)
+    # via gdc-client (pyproject.toml)
 requests==2.22.0
-    # via gdc_client (setup.py)
+    # via gdc-client (pyproject.toml)
 six==1.16.0
     # via
     #   progressbar2
     #   python-utils
 sortedcontainers==2.4.0
     # via intervaltree
 termcolor==1.1.0
-    # via gdc_client (setup.py)
+    # via gdc-client (pyproject.toml)
 urllib3==1.25.11
     # via requests
 zipp==3.17.0