Merge pull request #42 from cancervariants/eb

Update Package Requirements

.github/workflows/github-actions.yml

@@ -16,7 +16,7 @@ jobs:
             - name: Setup Python
               uses: actions/setup-python@v1
               with:
-                  python-version: 3.8
+                  python-version: 3.7
 
             - name: Install dependencies
               run: |

Pipfile

@@ -5,11 +5,9 @@ name = "pypi"
 
 [packages]
 pydantic = "*"
-twine = "*"
 fastapi = "*"
 uvicorn = "*"
 click = "*"
-civicpy = "*"
 boto3 = "*"
 beautifulsoup4 = "*"
 gffutils = "*"
@@ -34,4 +32,4 @@ pytest-cov = "*"
 jupyterlab = "*"
 
 [requires]
-python_version = "3.8"
+python_version = "3.7"

requirements-dev.txt

@@ -25,17 +25,16 @@ beautifulsoup4==4.9.3
 biocommons.seqrepo==0.6.3
 bioutils==0.5.2.post3; python_version >= '3.6'
 bleach==3.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-boto3==1.17.40
-botocore==1.20.40; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
+boto3==1.17.41
+botocore==1.20.41; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 bs4==0.0.1
 canonicaljson==1.4.0; python_version ~= '3.5'
 certifi==2020.12.5
 cffi==1.14.5
 cfgv==3.2.0; python_full_version >= '3.6.1'
 chardet==4.0.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-civicpy==1.1.3
+civicpy==1.1.3; python_version >= '3.5'
 click==7.1.2
-colorama==0.4.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 coloredlogs==15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 coverage==5.5
 coveralls==3.0.1
@@ -45,7 +44,6 @@ defusedxml==0.7.1; python_version >= '2.7' and python_version not in '3.0, 3.1,
 deprecation==2.1.0
 distlib==0.3.1
 docopt==0.6.2
-docutils==0.16; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 entrypoints==0.3; python_version >= '2.7'
 fake-useragent==0.1.11
 fastapi==0.63.0
@@ -60,25 +58,23 @@ httptools==0.1.1
 humanfriendly==9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 identify==2.2.2; python_full_version >= '3.6.1'
 idna==2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-importlib-metadata==3.10.0; python_version >= '3.6'
 inflection==0.5.1; python_version >= '3.5'
 iniconfig==1.1.1
-ipykernel==5.5.0; python_version >= '3.5'
+ipykernel==5.5.3; python_version >= '3.5'
 ipython-genutils==0.2.0
 ipython==7.22.0; python_version >= '3.7'
 jedi==0.18.0; python_version >= '3.6'
 jinja2==2.11.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'
+jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 json5==0.9.5
 jsonschema==3.2.0
 jupyter-client==6.1.12; python_version >= '3.5'
 jupyter-core==4.7.1; python_version >= '3.6'
 jupyter-packaging==0.7.12; python_version >= '3.6'
 jupyter-server==1.5.1; python_version >= '3.6'
 jupyterlab-pygments==0.1.2
-jupyterlab-server==2.3.0; python_version >= '3.6'
+jupyterlab-server==2.4.0; python_version >= '3.6'
 jupyterlab==3.0.12
-keyring==23.0.1; python_version >= '3.6'
 lxml==4.6.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 markdown==3.3.4; python_version >= '3.6'
 markupsafe==1.1.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
@@ -98,10 +94,9 @@ packaging==20.9; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.
 pandas==1.2.3; python_full_version >= '3.7.1'
 pandocfilters==1.4.3
 parse==1.19.0
-parso==0.8.1; python_version >= '3.6'
+parso==0.8.2; python_version >= '3.6'
 pexpect==4.8.0; sys_platform != 'win32'
 pickleshare==0.7.5
-pkginfo==1.7.0
 pluggy==0.13.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pre-commit==2.11.1
 prometheus-client==0.9.0
@@ -116,41 +111,37 @@ pyee==8.1.0
 pyfaidx==0.5.9.5
 pyflakes==2.3.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pygments==2.8.1; python_version >= '3.5'
-pyparsing==2.4.7; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'
+pyparsing==2.4.7; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pyppeteer==0.2.5; python_full_version >= '3.6.1' and python_full_version < '4.0.0'
 pyquery==1.4.3
 pyrsistent==0.17.3; python_version >= '3.5'
 pysam==0.16.0.1
 pytest-cov==2.11.1
 pytest==6.2.2
-python-dateutil==2.8.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
+python-dateutil==2.8.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 python-jsonschema-objects==0.3.10
 pytz==2021.1
 pyyaml==5.4.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 pyzmq==22.0.3; python_version >= '3.6'
-readme-renderer==29.0
 requests-html==0.10.0; python_version >= '3.6'
-requests-toolbelt==0.9.1
 requests==2.25.1
-rfc3986==1.4.0
 s3transfer==0.3.6
 send2trash==1.5.0
 seqrepo==0.0.0
-simplejson==3.17.2; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2'
-six==1.15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
+simplejson==3.17.2; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
+six==1.15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 sniffio==1.2.0; python_version >= '3.5'
 snowballstemmer==2.1.0
-soupsieve==2.2.1; python_version >= '3.0'
+soupsieve==2.2.1; python_version >= '3'
 sqlparse==0.4.1; python_version >= '3.5'
 starlette==0.13.6; python_version >= '3.6'
 tabulate==0.8.9
 terminado==0.9.4; python_version >= '3.6'
 testpath==0.4.4
-toml==0.10.2; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'
+toml==0.10.2; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 tornado==6.1; python_version >= '3.5'
 tqdm==4.59.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 traitlets==5.0.5; python_version >= '3.7'
-twine==3.4.1
 typing-extensions==3.7.4.3
 urllib3==1.26.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_full_version < '4.0.0'
 uvicorn==0.13.4
@@ -162,4 +153,3 @@ wcwidth==0.2.5
 webencodings==0.5.1
 websockets==8.1
 yoyo-migrations==7.3.1
-zipp==3.4.1; python_version >= '3.6'

requirements.txt

@@ -10,25 +10,18 @@ appdirs==1.4.4
 argcomplete==1.12.2
 argh==0.26.2
 attrs==20.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-backports-datetime-fromisoformat==1.0.0
 beautifulsoup4==4.9.3
 biocommons.seqrepo==0.6.3
 bioutils==0.5.2.post3; python_version >= '3.6'
-bleach==3.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-boto3==1.17.40
-botocore==1.20.40; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
+boto3==1.17.41
+botocore==1.20.41; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
 bs4==0.0.1
 canonicaljson==1.4.0; python_version ~= '3.5'
 certifi==2020.12.5
 chardet==4.0.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-civicpy==1.1.3
 click==7.1.2
-colorama==0.4.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 coloredlogs==15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 cssselect==1.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-decorator==4.4.2
-deprecation==2.1.0
-docutils==0.16; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 fake-useragent==0.1.11
 fastapi==0.63.0
 frozendict==1.2
@@ -38,55 +31,38 @@ h11==0.12.0; python_version >= '3.6'
 httptools==0.1.1
 humanfriendly==9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 idna==2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-importlib-metadata==3.10.0; python_version >= '3.6'
 inflection==0.5.1; python_version >= '3.5'
-jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'
+jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
 jsonschema==3.2.0
-keyring==23.0.1; python_version >= '3.6'
 lxml==4.6.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 markdown==3.3.4; python_version >= '3.6'
-networkx==2.5; python_version >= '3.6'
 numpy==1.20.2; python_version >= '3.7'
-obonet==0.2.6; python_version >= '3'
-packaging==20.9; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pandas==1.2.3; python_full_version >= '3.7.1'
 parse==1.19.0
-pkginfo==1.7.0
 pydantic==1.8.1
 pyee==8.1.0
 pyfaidx==0.5.9.5
-pygments==2.8.1; python_version >= '3.5'
-pyparsing==2.4.7; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'
 pyppeteer==0.2.5; python_full_version >= '3.6.1' and python_full_version < '4.0.0'
 pyquery==1.4.3
 pyrsistent==0.17.3; python_version >= '3.5'
 pysam==0.16.0.1
-python-dateutil==2.8.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
+python-dateutil==2.8.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 python-jsonschema-objects==0.3.10
-pytz==2021.1
 pyyaml==5.4.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
-readme-renderer==29.0
 requests-html==0.10.0; python_version >= '3.6'
-requests-toolbelt==0.9.1
 requests==2.25.1
-rfc3986==1.4.0
 s3transfer==0.3.6
 seqrepo==0.0.0
-simplejson==3.17.2; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2'
-six==1.15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
-soupsieve==2.2.1; python_version >= '3.0'
+simplejson==3.17.2; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
+six==1.15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+soupsieve==2.2.1; python_version >= '3'
 sqlparse==0.4.1; python_version >= '3.5'
 starlette==0.13.6; python_version >= '3.6'
 tabulate==0.8.9
 tqdm==4.59.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-twine==3.4.1
 typing-extensions==3.7.4.3
 urllib3==1.26.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_full_version < '4.0.0'
 uvicorn==0.13.4
 uvloop==0.15.2
-vcfpy==0.13.3
 w3lib==1.22.0
-webencodings==0.5.1
 websockets==8.1
 yoyo-migrations==7.3.1
-zipp==3.4.1; python_version >= '3.6'