so many more issues

hail-is · Apr 24, 2023 · 6916292 · 6916292
1 parent 49302a5
commit 6916292
Show file tree

Hide file tree

Showing 15 changed files with 161 additions and 400 deletions.
diff --git a/auth/pinned-requirements.txt b/auth/pinned-requirements.txt
@@ -1,6 +1,6 @@
 #
-# This file is autogenerated by pip-compile with python 3.7
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.8
+# by the following command:
 #
 #    pip-compile --output-file=hail/auth/pinned-requirements.txt hail/auth/requirements.txt
 #

diff --git a/batch/pinned-requirements.txt b/batch/pinned-requirements.txt
@@ -1,6 +1,6 @@
 #
-# This file is autogenerated by pip-compile with python 3.7
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.8
+# by the following command:
 #
 #    pip-compile --output-file=hail/batch/pinned-requirements.txt hail/batch/requirements.txt
 #
@@ -27,12 +27,6 @@ async-timeout==4.0.2
     #   -c hail/batch/../web_common/pinned-requirements.txt
     #   -r hail/batch/requirements.txt
     #   aiohttp
-asynctest==0.13.0
-    # via
-    #   -c hail/batch/../gear/pinned-requirements.txt
-    #   -c hail/batch/../hail/python/pinned-requirements.txt
-    #   -c hail/batch/../web_common/pinned-requirements.txt
-    #   aiohttp
 attrs==23.1.0
     # via
     #   -c hail/batch/../gear/pinned-requirements.txt
@@ -63,21 +57,14 @@ idna==3.4
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   -c hail/batch/../web_common/pinned-requirements.txt
     #   yarl
-importlib-metadata==3.10.1
-    # via
-    #   -c hail/batch/../gear/pinned-requirements.txt
-    #   -c hail/batch/../hail/python/dev/pinned-requirements.txt
-    #   -c hail/batch/../hail/python/pinned-requirements.txt
-    #   -c hail/batch/../web_common/pinned-requirements.txt
-    #   attrs
 multidict==6.0.4
     # via
     #   -c hail/batch/../gear/pinned-requirements.txt
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   -c hail/batch/../web_common/pinned-requirements.txt
     #   aiohttp
     #   yarl
-numpy==1.21.6
+numpy==1.24.3
     # via
     #   -c hail/batch/../hail/python/dev/pinned-requirements.txt
     #   -c hail/batch/../hail/python/pinned-requirements.txt
@@ -87,7 +74,7 @@ packaging==23.1
     #   -c hail/batch/../hail/python/dev/pinned-requirements.txt
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   plotly
-pandas==1.3.5
+pandas==2.0.1
     # via
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   -r hail/batch/requirements.txt
@@ -118,25 +105,16 @@ tenacity==8.2.2
     #   plotly
 typing-extensions==4.5.0
     # via
-    #   -c hail/batch/../gear/pinned-requirements.txt
     #   -c hail/batch/../hail/python/dev/pinned-requirements.txt
     #   -c hail/batch/../hail/python/pinned-requirements.txt
-    #   -c hail/batch/../web_common/pinned-requirements.txt
     #   aiodocker
-    #   aiohttp
-    #   async-timeout
-    #   importlib-metadata
-    #   yarl
-yarl==1.9.1
+tzdata==2023.3
     # via
-    #   -c hail/batch/../gear/pinned-requirements.txt
     #   -c hail/batch/../hail/python/pinned-requirements.txt
-    #   -c hail/batch/../web_common/pinned-requirements.txt
-    #   aiohttp
-zipp==3.15.0
+    #   pandas
+yarl==1.9.1
     # via
     #   -c hail/batch/../gear/pinned-requirements.txt
-    #   -c hail/batch/../hail/python/dev/pinned-requirements.txt
     #   -c hail/batch/../hail/python/pinned-requirements.txt
     #   -c hail/batch/../web_common/pinned-requirements.txt
-    #   importlib-metadata
+    #   aiohttp
diff --git a/batch/requirements.txt b/batch/requirements.txt
@@ -3,7 +3,7 @@
 -c ../gear/pinned-requirements.txt
 -c ../web_common/pinned-requirements.txt
 dictdiffer>=0.8.1,<1
-pandas>=1.3.0,<1.5.0
+pandas>2,<3
 plotly>=5.5.0,<6
 # Worker requirements
 aiodocker>=0.17.0,<1

diff --git a/ci/Dockerfile.ci-utils b/ci/Dockerfile.ci-utils
@@ -20,7 +20,7 @@ RUN hail-pip-install \
       -r hailtop-requirements.txt \
       -r gear-requirements.txt \
       twine==1.11.0 \
-      Jinja2==3.0.3
+      'Jinja2>3,<4'
 
 FROM golang:1.18 AS skopeo-build
 

diff --git a/ci/pinned-requirements.txt b/ci/pinned-requirements.txt
@@ -1,6 +1,6 @@
 #
-# This file is autogenerated by pip-compile with python 3.7
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.8
+# by the following command:
 #
 #    pip-compile --output-file=hail/ci/pinned-requirements.txt hail/ci/requirements.txt
 #
@@ -41,13 +41,6 @@ idna==3.4
     #   -c hail/ci/../hail/python/pinned-requirements.txt
     #   -c hail/ci/../web_common/pinned-requirements.txt
     #   requests
-importlib-metadata==3.10.1
-    # via
-    #   -c hail/ci/../gear/pinned-requirements.txt
-    #   -c hail/ci/../hail/python/dev/pinned-requirements.txt
-    #   -c hail/ci/../hail/python/pinned-requirements.txt
-    #   -c hail/ci/../web_common/pinned-requirements.txt
-    #   click
 matrix-client==0.4.0
     # via zulip
 pycparser==2.21
@@ -68,11 +61,8 @@ requests[security]==2.28.2
     #   zulip
 typing-extensions==4.5.0
     # via
-    #   -c hail/ci/../gear/pinned-requirements.txt
     #   -c hail/ci/../hail/python/dev/pinned-requirements.txt
     #   -c hail/ci/../hail/python/pinned-requirements.txt
-    #   -c hail/ci/../web_common/pinned-requirements.txt
-    #   importlib-metadata
     #   zulip
 uritemplate==4.1.1
     # via
@@ -85,12 +75,5 @@ urllib3==1.26.15
     #   -c hail/ci/../hail/python/pinned-requirements.txt
     #   matrix-client
     #   requests
-zipp==3.15.0
-    # via
-    #   -c hail/ci/../gear/pinned-requirements.txt
-    #   -c hail/ci/../hail/python/dev/pinned-requirements.txt
-    #   -c hail/ci/../hail/python/pinned-requirements.txt
-    #   -c hail/ci/../web_common/pinned-requirements.txt
-    #   importlib-metadata
 zulip==0.8.2
     # via -r hail/ci/requirements.txt
diff --git a/gear/pinned-requirements.txt b/gear/pinned-requirements.txt
@@ -1,6 +1,6 @@
 #
-# This file is autogenerated by pip-compile with python 3.7
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.8
+# by the following command:
 #
 #    pip-compile --output-file=hail/gear/pinned-requirements.txt hail/gear/requirements.txt
 #
@@ -24,11 +24,6 @@ async-timeout==4.0.2
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c hail/gear/../hail/python/pinned-requirements.txt
     #   aiohttp
-asynctest==0.13.0
-    # via
-    #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
-    #   -c hail/gear/../hail/python/pinned-requirements.txt
-    #   aiohttp
 attrs==23.1.0
     # via
     #   -c hail/gear/../hail/python/dev/pinned-requirements.txt
@@ -97,12 +92,6 @@ idna==3.4
     #   -c hail/gear/../hail/python/pinned-requirements.txt
     #   requests
     #   yarl
-importlib-metadata==3.10.1
-    # via
-    #   -c hail/gear/../hail/python/dev/pinned-requirements.txt
-    #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
-    #   -c hail/gear/../hail/python/pinned-requirements.txt
-    #   attrs
 kubernetes-asyncio==19.15.1
     # via -r hail/gear/requirements.txt
 multidict==6.0.4
@@ -124,7 +113,6 @@ protobuf==3.20.2
     #   -c hail/gear/../hail/python/pinned-requirements.txt
     #   google-api-core
     #   google-cloud-profiler
-    #   googleapis-common-protos
 pyasn1==0.5.0
     # via
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
@@ -152,6 +140,7 @@ python-dateutil==2.8.2
     #   kubernetes-asyncio
 pyyaml==6.0
     # via
+    #   -c hail/gear/../hail/python/dev/pinned-requirements.txt
     #   -c hail/gear/../hail/python/pinned-requirements.txt
     #   kubernetes-asyncio
 requests==2.28.2
@@ -180,16 +169,6 @@ sortedcontainers==2.4.0
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c hail/gear/../hail/python/pinned-requirements.txt
     #   -r hail/gear/requirements.txt
-typing-extensions==4.5.0
-    # via
-    #   -c hail/gear/../hail/python/dev/pinned-requirements.txt
-    #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
-    #   -c hail/gear/../hail/python/pinned-requirements.txt
-    #   aiohttp
-    #   aiohttp-session
-    #   async-timeout
-    #   importlib-metadata
-    #   yarl
 uritemplate==4.1.1
     # via google-api-python-client
 urllib3==1.26.15
@@ -209,12 +188,6 @@ yarl==1.9.1
     #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c hail/gear/../hail/python/pinned-requirements.txt
     #   aiohttp
-zipp==3.15.0
-    # via
-    #   -c hail/gear/../hail/python/dev/pinned-requirements.txt
-    #   -c hail/gear/../hail/python/hailtop/pinned-requirements.txt
-    #   -c hail/gear/../hail/python/pinned-requirements.txt
-    #   importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file:
 # setuptools