Update pip requirements

  - Bump certifi version
  - Remove unused coveralls dependency

api/requirements.in

@@ -23,3 +23,4 @@ apscheduler
 django-computedfields>=0.1.5
 pyyaml>=5.4
 sqlparse>=0.4.2
+certifi==2023.7.22

api/requirements.txt

@@ -1,56 +1,57 @@
 #
-# This file is autogenerated by pip-compile with python 3.9
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.8
+# by the following command:
 #
-#    pip-compile --annotation-style=line api/requirements.in
+#    pip-compile --annotation-style=line requirements.in
 #
-apscheduler==3.10.0       # via -r api/requirements.in
+apscheduler==3.10.0       # via -r requirements.in
 asgiref==3.6.0            # via django
-boto3==1.26.68            # via -r api/requirements.in
+backports-zoneinfo==0.2.1  # via pytz-deprecation-shim, tzlocal
+boto3==1.26.68            # via -r requirements.in
 botocore==1.29.68         # via boto3, s3transfer
-certifi==2022.12.7        # via requests
+certifi==2023.7.22        # via -r requirements.in, requests
 charset-normalizer==3.0.1  # via requests
-coreapi==2.3.3            # via -r api/requirements.in, drf-yasg
+coreapi==2.3.3            # via -r requirements.in, drf-yasg
 coreschema==0.0.4         # via coreapi, drf-yasg
-coverage==7.1.0           # via -r api/requirements.in
-django==3.2.17            # via -r api/requirements.in, django-computedfields, django-cors-headers, django-fast-update, django-filter, django-nine, djangorestframework, djangorestframework-hstore, drf-yasg
-django-computedfields==0.2.1  # via -r api/requirements.in
-django-cors-headers==3.13.0  # via -r api/requirements.in
-django-elasticsearch-dsl==6.5.0  # via -r api/requirements.in, django-elasticsearch-dsl-drf
-django-elasticsearch-dsl-drf==0.22.5  # via -r api/requirements.in
+coverage==7.1.0           # via -r requirements.in
+django==3.2.17            # via -r requirements.in, django-computedfields, django-cors-headers, django-fast-update, django-filter, django-nine, djangorestframework, djangorestframework-hstore, drf-yasg
+django-computedfields==0.2.1  # via -r requirements.in
+django-cors-headers==3.13.0  # via -r requirements.in
+django-elasticsearch-dsl==6.5.0  # via -r requirements.in, django-elasticsearch-dsl-drf
+django-elasticsearch-dsl-drf==0.22.5  # via -r requirements.in
 django-fast-update==0.2.1  # via django-computedfields
-django-filter==22.1       # via -r api/requirements.in
+django-filter==22.1       # via -r requirements.in
 django-hstore==1.4.2      # via djangorestframework-hstore
 django-nine==0.2.7        # via django-elasticsearch-dsl-drf
-djangorestframework==3.13.1  # via -r api/requirements.in, django-elasticsearch-dsl-drf, djangorestframework-hstore, drf-yasg
-djangorestframework-hstore==1.3  # via -r api/requirements.in
-drf-yasg==1.21.5          # via -r api/requirements.in
+djangorestframework==3.13.1  # via -r requirements.in, django-elasticsearch-dsl-drf, djangorestframework-hstore, drf-yasg
+djangorestframework-hstore==1.3  # via -r requirements.in
+drf-yasg==1.21.5          # via -r requirements.in
 elasticsearch==6.8.2      # via django-elasticsearch-dsl-drf, elasticsearch-dsl
-elasticsearch-dsl==6.4.0  # via -r api/requirements.in, django-elasticsearch-dsl, django-elasticsearch-dsl-drf
+elasticsearch-dsl==6.4.0  # via -r requirements.in, django-elasticsearch-dsl, django-elasticsearch-dsl-drf
 idna==3.4                 # via requests
 inflection==0.5.1         # via drf-yasg
 itypes==1.2.0             # via coreapi
-jinja2==3.1.2             # via -r api/requirements.in, coreschema
+jinja2==3.1.2             # via -r requirements.in, coreschema
 jmespath==1.0.1           # via boto3, botocore
-markupsafe==2.1.2         # via -r api/requirements.in, jinja2
+markupsafe==2.1.2         # via -r requirements.in, jinja2
 packaging==23.0           # via django-nine, drf-yasg
 psycopg2==2.9.5           # via djangorestframework-hstore
-psycopg2-binary==2.9.5    # via -r api/requirements.in
+psycopg2-binary==2.9.5    # via -r requirements.in
 python-dateutil==2.8.2    # via botocore, elasticsearch-dsl
 pytz==2022.7.1            # via apscheduler, django, djangorestframework, drf-yasg
 pytz-deprecation-shim==0.1.0.post0  # via tzlocal
-pyyaml==6.0               # via -r api/requirements.in
-requests==2.28.2          # via -r api/requirements.in, coreapi
+pyyaml==6.0               # via -r requirements.in
+requests==2.28.2          # via -r requirements.in, coreapi
 ruamel-yaml==0.17.21      # via drf-yasg
 ruamel-yaml-clib==0.2.7   # via ruamel-yaml
 s3transfer==0.6.0         # via boto3
-six==1.16.0               # via -r api/requirements.in, apscheduler, django-elasticsearch-dsl, django-elasticsearch-dsl-drf, elasticsearch-dsl, python-dateutil
-sqlparse==0.4.3           # via -r api/requirements.in, django
+six==1.16.0               # via -r requirements.in, apscheduler, django-elasticsearch-dsl, django-elasticsearch-dsl-drf, elasticsearch-dsl, python-dateutil
+sqlparse==0.4.3           # via -r requirements.in, django
 typing-extensions==4.4.0  # via django-computedfields
 tzdata==2022.7            # via pytz-deprecation-shim
 tzlocal==4.2              # via apscheduler
 uritemplate==4.1.1        # via coreapi, drf-yasg
-urllib3==1.26.14          # via -r api/requirements.in, botocore, elasticsearch, requests
+urllib3==1.26.14          # via -r requirements.in, botocore, elasticsearch, requests
 
 # The following packages are considered to be unsafe in a requirements file:
 # setuptools

common/requirements.in

@@ -18,3 +18,4 @@ pyyaml>=5.4
 sqlparse>=0.4.2
 markupsafe==2.0.0
 rpy2==3.4.5
+certifi==2023.7.22

common/requirements.txt

@@ -1,50 +1,51 @@
 #
-# This file is autogenerated by pip-compile with python 3.9
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.8
+# by the following command:
 #
-#    pip-compile --annotation-style=line common/requirements.in
+#    pip-compile --annotation-style=line requirements.in
 #
 asgiref==3.6.0            # via django
-boto3==1.26.71            # via -r common/requirements.in
+backports-zoneinfo==0.2.1  # via pytz-deprecation-shim, tzlocal
+boto3==1.26.71            # via -r requirements.in
 botocore==1.29.71         # via boto3, s3transfer
-certifi==2022.12.7        # via requests
+certifi==2023.7.22        # via -r requirements.in, requests
 cffi==1.15.1              # via rpy2
 charset-normalizer==3.0.1  # via requests
-coverage==7.1.0           # via -r common/requirements.in
-daiquiri==3.2.1           # via -r common/requirements.in
-django==3.2.18            # via -r common/requirements.in, django-computedfields, django-fast-update, django-nine, djangorestframework
-django-computedfields==0.2.1  # via -r common/requirements.in
-django-elasticsearch-dsl==6.5.0  # via -r common/requirements.in, django-elasticsearch-dsl-drf
-django-elasticsearch-dsl-drf==0.22.5  # via -r common/requirements.in
+coverage==7.1.0           # via -r requirements.in
+daiquiri==3.2.1           # via -r requirements.in
+django==3.2.18            # via -r requirements.in, django-computedfields, django-fast-update, django-nine, djangorestframework
+django-computedfields==0.2.1  # via -r requirements.in
+django-elasticsearch-dsl==6.5.0  # via -r requirements.in, django-elasticsearch-dsl-drf
+django-elasticsearch-dsl-drf==0.22.5  # via -r requirements.in
 django-fast-update==0.2.1  # via django-computedfields
 django-nine==0.2.7        # via django-elasticsearch-dsl-drf
-djangorestframework==3.13.1  # via -r common/requirements.in, django-elasticsearch-dsl-drf
+djangorestframework==3.13.1  # via -r requirements.in, django-elasticsearch-dsl-drf
 elasticsearch==6.8.2      # via django-elasticsearch-dsl-drf, elasticsearch-dsl
-elasticsearch-dsl==6.4.0  # via -r common/requirements.in, django-elasticsearch-dsl, django-elasticsearch-dsl-drf
+elasticsearch-dsl==6.4.0  # via -r requirements.in, django-elasticsearch-dsl, django-elasticsearch-dsl-drf
 idna==3.4                 # via requests, yarl
 jinja2==3.1.2             # via rpy2
 jmespath==1.0.1           # via boto3, botocore
-markupsafe==2.0.0         # via -r common/requirements.in, jinja2
+markupsafe==2.0.0         # via -r requirements.in, jinja2
 multidict==6.0.4          # via yarl
 packaging==23.0           # via django-nine
-psycopg2-binary==2.9.5    # via -r common/requirements.in
+psycopg2-binary==2.9.5    # via -r requirements.in
 pycparser==2.21           # via cffi
 python-dateutil==2.8.2    # via botocore, elasticsearch-dsl
 python-json-logger==2.0.6  # via daiquiri
 pytz==2022.7.1            # via django, djangorestframework, rpy2
 pytz-deprecation-shim==0.1.0.post0  # via tzlocal
-pyyaml==6.0               # via -r common/requirements.in, vcrpy
-raven==6.10.0             # via -r common/requirements.in
-requests==2.28.2          # via -r common/requirements.in
-retrying==1.3.4           # via -r common/requirements.in
-rpy2==3.4.5               # via -r common/requirements.in
+pyyaml==6.0               # via -r requirements.in, vcrpy
+raven==6.10.0             # via -r requirements.in
+requests==2.28.2          # via -r requirements.in
+retrying==1.3.4           # via -r requirements.in
+rpy2==3.4.5               # via -r requirements.in
 s3transfer==0.6.0         # via boto3
 six==1.16.0               # via django-elasticsearch-dsl, django-elasticsearch-dsl-drf, elasticsearch-dsl, python-dateutil, retrying, vcrpy
-sqlparse==0.4.3           # via -r common/requirements.in, django
+sqlparse==0.4.3           # via -r requirements.in, django
 typing-extensions==4.5.0  # via django-computedfields
 tzdata==2022.7            # via pytz-deprecation-shim
 tzlocal==4.2              # via rpy2
-urllib3==1.26.14          # via -r common/requirements.in, botocore, elasticsearch, requests
-vcrpy==4.2.1              # via -r common/requirements.in
+urllib3==1.26.14          # via -r requirements.in, botocore, elasticsearch, requests
+vcrpy==4.2.1              # via -r requirements.in
 wrapt==1.14.1             # via vcrpy
-yarl==1.8.2               # via vcrpy
+yarl==1.8.2               # via vcrp

foreman/requirements.in

@@ -22,3 +22,4 @@ numpy==1.19.5
 pandas==1.1.5
 scipy
 sqlparse
+certifi==2023.7.22

foreman/requirements.txt

@@ -1,46 +1,46 @@
 #
-# This file is autogenerated by pip-compile with python 3.9
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.8
+# by the following command:
 #
-#    pip-compile --annotation-style=line foreman/requirements.in
+#    pip-compile --annotation-style=line requirements.in
 #
 asgiref==3.6.0            # via django
-certifi==2022.12.7        # via requests
+certifi==2023.7.22        # via -r requirements.in, requests
 charset-normalizer==3.0.1  # via requests
 click==8.1.3              # via pyrefinebio
-coverage==7.1.0           # via -r foreman/requirements.in
-django==3.2.17            # via -r foreman/requirements.in, django-computedfields, django-fast-update, django-nine, djangorestframework
-django-computedfields==0.2.1  # via -r foreman/requirements.in
-django-elasticsearch-dsl==6.5.0  # via -r foreman/requirements.in, django-elasticsearch-dsl-drf
-django-elasticsearch-dsl-drf==0.22.5  # via -r foreman/requirements.in
+coverage==7.1.0           # via -r requirements.in
+django==3.2.17            # via -r requirements.in, django-computedfields, django-fast-update, django-nine, djangorestframework
+django-computedfields==0.2.1  # via -r requirements.in
+django-elasticsearch-dsl==6.5.0  # via -r requirements.in, django-elasticsearch-dsl-drf
+django-elasticsearch-dsl-drf==0.22.5  # via -r requirements.in
 django-fast-update==0.2.1  # via django-computedfields
 django-nine==0.2.7        # via django-elasticsearch-dsl-drf
-djangorestframework==3.13.1  # via -r foreman/requirements.in, django-elasticsearch-dsl-drf
+djangorestframework==3.13.1  # via -r requirements.in, django-elasticsearch-dsl-drf
 elasticsearch==6.8.2      # via django-elasticsearch-dsl-drf, elasticsearch-dsl
-elasticsearch-dsl==6.4.0  # via -r foreman/requirements.in, django-elasticsearch-dsl, django-elasticsearch-dsl-drf
-geoparse==2.0.3           # via -r foreman/requirements.in
+elasticsearch-dsl==6.4.0  # via -r requirements.in, django-elasticsearch-dsl, django-elasticsearch-dsl-drf
+geoparse==2.0.3           # via -r requirements.in
 idna==3.4                 # via requests, yarl
 iso8601==1.1.0            # via pyrefinebio
 multidict==6.0.4          # via yarl
-numpy==1.19.5             # via -r foreman/requirements.in, geoparse, pandas, scipy
+numpy==1.19.5             # via -r requirements.in, geoparse, pandas, scipy
 packaging==23.0           # via django-nine
-pandas==1.1.5             # via -r foreman/requirements.in, geoparse
-psycopg2-binary==2.9.5    # via -r foreman/requirements.in
-pyrefinebio==0.4.9        # via -r foreman/requirements.in
-python-dateutil==2.8.2    # via -r foreman/requirements.in, elasticsearch-dsl, pandas
+pandas==1.1.5             # via -r requirements.in, geoparse
+psycopg2-binary==2.9.5    # via -r requirements.in
+pyrefinebio==0.4.9        # via -r requirements.in
+python-dateutil==2.8.2    # via -r requirements.in, elasticsearch-dsl, pandas
 pytimeparse==1.1.8        # via pyrefinebio
 pytz==2022.7.1            # via django, djangorestframework, pandas
-pyyaml==6.0               # via -r foreman/requirements.in, pyrefinebio, vcrpy
-raven==6.10.0             # via -r foreman/requirements.in
-requests==2.28.2          # via -r foreman/requirements.in, geoparse, pyrefinebio
-retrying==1.3.4           # via -r foreman/requirements.in
-scipy==1.10.0             # via -r foreman/requirements.in
+pyyaml==6.0               # via -r requirements.in, pyrefinebio, vcrpy
+raven==6.10.0             # via -r requirements.in
+requests==2.28.2          # via -r requirements.in, geoparse, pyrefinebio
+retrying==1.3.4           # via -r requirements.in
+scipy==1.10.0             # via -r requirements.in
 six==1.16.0               # via django-elasticsearch-dsl, django-elasticsearch-dsl-drf, elasticsearch-dsl, python-dateutil, retrying, vcrpy
-sqlparse==0.4.3           # via -r foreman/requirements.in, django
-tblib==1.7.0              # via -r foreman/requirements.in
+sqlparse==0.4.3           # via -r requirements.in, django
+tblib==1.7.0              # via -r requirements.in
 tqdm==4.64.1              # via geoparse
 typing-extensions==4.4.0  # via django-computedfields
 urllib3==1.26.14          # via elasticsearch, requests
-vcrpy==4.2.1              # via -r foreman/requirements.in
+vcrpy==4.2.1              # via -r requirements.in
 wrapt==1.14.1             # via vcrpy
 yarl==1.8.2               # via vcrpy

workers/data_refinery_workers/downloaders/requirements.in

@@ -3,10 +3,10 @@ requests>=2.23.0
 urllib3>=1.24.2
 psycopg2-binary>=2.8.4
 retrying
-coveralls
 psutil>=5.6.6
 vcrpy
 django-computedfields>=0.1.5
 pyyaml>=5.4
 sqlparse>=0.4.2
 rpy2==3.4.5
+certifi==2023.7.22

workers/data_refinery_workers/downloaders/requirements.txt

@@ -1,38 +1,36 @@
 #
-# This file is autogenerated by pip-compile with python 3.9
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.8
+# by the following command:
 #
-#    pip-compile --annotation-style=line workers/data_refinery_workers/downloaders/requirements.in
+#    pip-compile --annotation-style=line requirements.in
 #
 asgiref==3.6.0            # via django
-certifi==2022.12.7        # via requests
+backports-zoneinfo==0.2.1  # via pytz-deprecation-shim, tzlocal
+certifi==2023.7.22        # via -r requirements.in, requests
 cffi==1.15.1              # via rpy2
 charset-normalizer==3.0.1  # via requests
-coverage==6.5.0           # via coveralls
-coveralls==3.3.1          # via -r workers/data_refinery_workers/downloaders/requirements.in
-django==3.2.18            # via -r workers/data_refinery_workers/downloaders/requirements.in, django-computedfields, django-fast-update
-django-computedfields==0.2.1  # via -r workers/data_refinery_workers/downloaders/requirements.in
+django==3.2.18            # via -r requirements.in, django-computedfields, django-fast-update
+django-computedfields==0.2.1  # via -r requirements.in
 django-fast-update==0.2.1  # via django-computedfields
-docopt==0.6.2             # via coveralls
 idna==3.4                 # via requests, yarl
 jinja2==3.1.2             # via rpy2
 markupsafe==2.1.2         # via jinja2
 multidict==6.0.4          # via yarl
-psutil==5.9.4             # via -r workers/data_refinery_workers/downloaders/requirements.in
-psycopg2-binary==2.9.5    # via -r workers/data_refinery_workers/downloaders/requirements.in
+psutil==5.9.4             # via -r requirements.in
+psycopg2-binary==2.9.5    # via -r requirements.in
 pycparser==2.21           # via cffi
 pytz==2022.7.1            # via django, rpy2
 pytz-deprecation-shim==0.1.0.post0  # via tzlocal
-pyyaml==6.0               # via -r workers/data_refinery_workers/downloaders/requirements.in, vcrpy
-requests==2.28.2          # via -r workers/data_refinery_workers/downloaders/requirements.in, coveralls
-retrying==1.3.4           # via -r workers/data_refinery_workers/downloaders/requirements.in
-rpy2==3.4.5               # via -r workers/data_refinery_workers/downloaders/requirements.in
+pyyaml==6.0               # via -r requirements.in, vcrpy
+requests==2.28.2          # via -r requirements.in
+retrying==1.3.4           # via -r requirements.in
+rpy2==3.4.5               # via -r requirements.in
 six==1.16.0               # via retrying, vcrpy
-sqlparse==0.4.3           # via -r workers/data_refinery_workers/downloaders/requirements.in, django
+sqlparse==0.4.3           # via -r requirements.in, django
 typing-extensions==4.5.0  # via django-computedfields
 tzdata==2022.7            # via pytz-deprecation-shim
 tzlocal==4.2              # via rpy2
-urllib3==1.26.14          # via -r workers/data_refinery_workers/downloaders/requirements.in, requests
-vcrpy==4.2.1              # via -r workers/data_refinery_workers/downloaders/requirements.in
+urllib3==1.26.14          # via -r requirements.in, requests
+vcrpy==4.2.1              # via -r requirements.in
 wrapt==1.14.1             # via vcrpy
 yarl==1.8.2               # via vcrpy

workers/data_refinery_workers/processors/requirements.in

@@ -1,5 +1,4 @@
 boto3>=1.9.199
-coveralls
 django>=3.2,<4
 rpy2===3.4.5
 matplotlib
@@ -32,3 +31,4 @@ django-computedfields>=0.1.5
 pyyaml>=5.4
 sqlparse>=0.4.2
 nose
+certifi==2023.7.22