From 3b6c46ba8699bd9dabd627b8f4b3cd191ea03f4b Mon Sep 17 00:00:00 2001
From: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
Date: Fri, 30 Oct 2020 10:47:12 -0500
Subject: [PATCH] Fix dependency issues in compatibility tests (#1951)

* update reqs

* pin scanpy

* merge in fix for race conditions
---
 .github/workflows/compatibility_tests.yml | 2 +-
 server/requirements-dev.txt               | 1 -
 server/requirements-prepare.txt           | 1 -
 server/requirements.txt                   | 7 ++++---
 server/test/unit/auth/test_oauth.py       | 1 -
 5 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/compatibility_tests.yml b/.github/workflows/compatibility_tests.yml
index 99a3698d..fff70efa 100644
--- a/.github/workflows/compatibility_tests.yml
+++ b/.github/workflows/compatibility_tests.yml
@@ -28,7 +28,7 @@ jobs:
     continue-on-error: true
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7] # As of Oct 2020 Anndata is not compatible with 3.8
         anndata-version: [0.7.0, 0.7.1, 0.7.2, 0.7.3, 0.7.4]
         test-suite: [smoke-test, smoke-test-annotations]
     steps:
diff --git a/server/requirements-dev.txt b/server/requirements-dev.txt
index 0882128a..9f4fd724 100644
--- a/server/requirements-dev.txt
+++ b/server/requirements-dev.txt
@@ -6,6 +6,5 @@ parameterized>=0.7.0
 psycopg2-binary>=2.8.5
 pytest>=3.6.3
 python-jose>=3.2.0
-scanpy>=1.4.6
 twine>=1.12.1
 -r requirements.txt
diff --git a/server/requirements-prepare.txt b/server/requirements-prepare.txt
index 630015df..254f827b 100644
--- a/server/requirements-prepare.txt
+++ b/server/requirements-prepare.txt
@@ -1,3 +1,2 @@
-scanpy>=1.3.7
 python-igraph
 louvain>=0.6
diff --git a/server/requirements.txt b/server/requirements.txt
index d288aee8..7aeec71a 100644
--- a/server/requirements.txt
+++ b/server/requirements.txt
@@ -13,12 +13,13 @@ flatten-dict>=0.2.0
 fsspec>=0.4.4,<0.8.0
 gunicorn>=20.0.4
 numba>=0.49.1
-numpy>=1.16.0
+numpy>=1.15.0
 packaging>=20.0
-pandas>=0.24.2
+pandas>=1.0,!=1.1  # pandas 1.1 breaks tests, https://github.com/pandas-dev/pandas/issues/35446
 PyYAML>=5.3
-scipy>=1.3.0
+scipy>=1.0
 requests>=2.22.0
 tiledb>=0.5.9,>=0.6.2
 s3fs==0.4.2
+scanpy==1.4.6 # Until we move to anndata 0.7.4 scanpy needs to be pinned here
 sqlalchemy>=1.3.18
diff --git a/server/test/unit/auth/test_oauth.py b/server/test/unit/auth/test_oauth.py
index b5214767..be6ab850 100644
--- a/server/test/unit/auth/test_oauth.py
+++ b/server/test/unit/auth/test_oauth.py
@@ -62,7 +62,6 @@ def jwks():
     data = dict(alg="RS256", kty="RSA", use="sig", kid="fake_kid",)
     return make_response(jsonify(dict(keys=[data])))
 
-
 # The port that the mock oauth server will listen on
 PORT = random.randint(10000, 12000)