DEV-2882 update deps (#293)

* upgrade pytest

* add pytest config in pyproject.toml

* add github action for prcess

* upgrade moto， httmock, requests-mock, flask, jsonschema, lxml, requests, pyyaml 

* remove dev-requiremetns.txt

* add markupsafe==2.0.1

* remove deps,  ndg-httpsclient~=0.5.0, pyasn1 pyopenssl, cryptography, python-jose

* update pytest config

pyproject.toml

@@ -40,3 +40,24 @@ skip = [".gitignore", ".dockerignore"]
 
 [tool.setuptools_scm]
 local_scheme = "dirty-tag"
+
+
+[tool.pytest.ini_options]
+minversion = 6.0
+python_files = "test_*.py"
+python_functions = "test_*"
+junit_family = "xunit2"
+junit_logging = "system-out"
+console_output_style = "classic"
+log_level = "ERROR"
+log_cli = "true"
+addopts = "-rfE --color=yes -p no:ddtrace -p no:ddtrace.pytest_bdd --cov=gdc_client --cov-report term"
+norecursedirs = [
+  ".git",
+  ".tox",
+  "dist",
+  "build"
+]
+testpaths = [
+  "tests",
+]

requirements.txt

@@ -4,46 +4,48 @@
 #
 #    pip-compile
 #
+attrs==23.2.0
+    # via
+    #   jsonschema
+    #   referencing
 certifi==2024.7.4
     # via requests
-cffi==1.15.1
-    # via cryptography
-chardet==3.0.4
+charset-normalizer==3.3.2
     # via requests
-cryptography==43.0.0
-    # via
-    #   gdc-client (pyproject.toml)
-    #   pyopenssl
 idna==2.8
     # via requests
 importlib-metadata==7.0.1
     # via gdc-client (pyproject.toml)
+importlib-resources==6.4.0
+    # via
+    #   jsonschema
+    #   jsonschema-specifications
 intervaltree==3.0.2
     # via gdc-client (pyproject.toml)
-jsonschema==2.6.0
+jsonschema==4.23.0
     # via gdc-client (pyproject.toml)
-lxml==4.4.2
-    # via gdc-client (pyproject.toml)
-ndg-httpsclient==0.5.0
+jsonschema-specifications==2023.12.1
+    # via jsonschema
+lxml==5.2.2
     # via gdc-client (pyproject.toml)
+pkgutil-resolve-name==1.3.10
+    # via jsonschema
 progressbar2==3.55.0
     # via gdc-client (pyproject.toml)
-pyasn1==0.4.8
-    # via
-    #   gdc-client (pyproject.toml)
-    #   ndg-httpsclient
-pycparser==2.21
-    # via cffi
-pyopenssl==24.2.1
-    # via
-    #   gdc-client (pyproject.toml)
-    #   ndg-httpsclient
 python-utils==2.7.1
     # via progressbar2
-pyyaml==5.3.1
+pyyaml==6.0.1
     # via gdc-client (pyproject.toml)
-requests==2.22.0
+referencing==0.35.1
+    # via
+    #   jsonschema
+    #   jsonschema-specifications
+requests==2.32.3
     # via gdc-client (pyproject.toml)
+rpds-py==0.19.1
+    # via
+    #   jsonschema
+    #   referencing
 six==1.16.0
     # via
     #   progressbar2
@@ -55,4 +57,6 @@ termcolor==1.1.0
 urllib3==1.25.11
     # via requests
 zipp==3.17.0
-    # via importlib-metadata
+    # via
+    #   importlib-metadata
+    #   importlib-resources

setup.cfg

@@ -15,7 +15,7 @@ classifiers =
     Programming Language :: Python
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3.8
-	Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.9
     License :: OSI Approved :: Apache Software License
     Topic :: Internet :: WWW/HTTP
 
@@ -25,17 +25,13 @@ package_dir =
     =src
 python_requires = >=3.8
 install_requires =
-    cryptography
-    jsonschema~=2.6.0
-    lxml~=4.4.2
-    ndg-httpsclient~=0.5.0
-    pyasn1
-    pyOpenSSL
-    PyYAML>=5.1
+    jsonschema
+    lxml
+    PyYAML>=6.0.1
     intervaltree~=3.0.2
     importlib_metadata
     termcolor~=1.1.0
-    requests~=2.22.0
+    requests
     progressbar2
 
 [options.packages.find]
@@ -46,15 +42,12 @@ where = src
 [options.extras_require]
 dev =
     click>= 8
-    flask~=1.0.2
-    pytest~=4.6.2
+    flask
+    pytest
     pytest-cov
-    requests-mock~=1.5.2
-    moto~=1.3.14
-    python-jose<3.3.0       # lower the requirements for cryptography, so python3.5 could work
-    httmock~=1.3.0
-    cfn-lint<0.22.0  # required by moto, limit version for jsonschema
-    aws-sam-translator<1.12.0a
+    requests-mock
+    moto
+    httmock
 
 [options.entry_points]
 console_scripts =

src/gdc_client/cli.py

@@ -12,18 +12,6 @@
 from gdc_client.common.config import GDCClientConfigShared, GDCClientArgumentParser
 
 
-####################################################
-# These packages are important but PyInstaller won't
-# bundle them unless they are imported
-import cffi
-import cryptography
-import OpenSSL
-import ndg.httpsclient
-import pyasn1
-
-####################################################
-
-
 DESCRIPTION = """
 The Genomic Data Commons Command Line Client
 """