From f3665f6b5336b0c3db390c7c1146354d0b9f2694 Mon Sep 17 00:00:00 2001
From: Kelvin <26215587+zktuong@users.noreply.github.com>
Date: Thu, 21 Apr 2022 20:12:07 +0100
Subject: [PATCH 01/11] Update tests.yml

---
 .github/workflows/tests.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 3fbfdda55..2221a85d1 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -106,7 +106,7 @@ jobs:
       shell: bash -l {0}
 
     - name: Set up R
-      uses: r-lib/actions/setup-r@v1
+      uses: r-lib/actions/setup-r@v2
       with:
         r-version: ${{ steps.R.outputs.version}}
 
@@ -153,6 +153,7 @@ jobs:
         remotes::install_cran("BiocManager")
         BiocManager::install(version = ${{ steps.R.outputs.biocversion}}, ask = FALSE)
         BiocManager::install(c('Biostrings', 'GenomicAlignments', 'IRanges'))
+        install.packages('matrixStats')
         install.packages(c('shazam', 'alakazam', 'tigger', 'airr', 'optparse'))
       shell: Rscript {0}
 

From b66ef695dab4a4cfe7cc6d54a419e854d879cec5 Mon Sep 17 00:00:00 2001
From: Kelvin <26215587+zktuong@users.noreply.github.com>
Date: Thu, 21 Apr 2022 21:56:21 +0100
Subject: [PATCH 02/11] Update tests.yml

does this work?
---
 .github/workflows/tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 2221a85d1..cbd56c0b2 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -25,8 +25,8 @@ jobs:
           - { python-version: 3.7, os: ubuntu-latest }
           - { python-version: 3.8, os: ubuntu-latest }
           - { python-version: 3.9, os: ubuntu-latest }
-          - { python-version: 3.7, os: macos-latest }
-          - { python-version: 3.8, os: macos-latest }
+          - { python-version: 3.7, os: macOS-11/20220419.3 }
+          - { python-version: 3.8, os: macOS-11/20220419.3 }
           # - { python-version: 3.9, os: macos-latest } # segmentation fault due to missing py3.9 macOSX wheel https://github.com/rpy2/rpy2/issues/846
           # disabled until it's fixed.
     runs-on: ${{ matrix.config.os }}

From e829ccd04019aac5e03044b09432c53a3830bcba Mon Sep 17 00:00:00 2001
From: Kelvin <26215587+zktuong@users.noreply.github.com>
Date: Thu, 21 Apr 2022 22:04:51 +0100
Subject: [PATCH 03/11] Update test_preprocessing.py

maybe this is the issue?
---
 tests/test_preprocessing.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/tests/test_preprocessing.py b/tests/test_preprocessing.py
index ea7db2dfb..acd7693ca 100644
--- a/tests/test_preprocessing.py
+++ b/tests/test_preprocessing.py
@@ -8,13 +8,12 @@
 from fixtures import (fasta_10x, annotation_10x, create_testfolder,
                       database_paths, dummy_adata, processed_files)
 
-try:
-    os.environ.pop('IGDATA')
-    os.environ.pop('GERMLINE')
-    os.environ.pop('BLASTDB')
-except:
-    pass
-
+if 'IGDATA' in os.environ:
+    del os.environ["IGDATA"]
+if 'GERMLINE' in os.environ:
+    del os.environ["GERMLINE"]
+if 'GERMLINE' in os.environ:
+    del os.environ["GERMLINE"]
 
 @pytest.mark.parametrize("filename,expected",
                          [pytest.param('filtered', 1),

From 610d7fc076a8337c0ce71be9fc0371872a8c0aa0 Mon Sep 17 00:00:00 2001
From: Kelvin <26215587+zktuong@users.noreply.github.com>
Date: Thu, 21 Apr 2022 22:04:58 +0100
Subject: [PATCH 04/11] Revert "Update tests.yml"

This reverts commit b66ef695dab4a4cfe7cc6d54a419e854d879cec5.
---
 .github/workflows/tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index cbd56c0b2..2221a85d1 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -25,8 +25,8 @@ jobs:
           - { python-version: 3.7, os: ubuntu-latest }
           - { python-version: 3.8, os: ubuntu-latest }
           - { python-version: 3.9, os: ubuntu-latest }
-          - { python-version: 3.7, os: macOS-11/20220419.3 }
-          - { python-version: 3.8, os: macOS-11/20220419.3 }
+          - { python-version: 3.7, os: macos-latest }
+          - { python-version: 3.8, os: macos-latest }
           # - { python-version: 3.9, os: macos-latest } # segmentation fault due to missing py3.9 macOSX wheel https://github.com/rpy2/rpy2/issues/846
           # disabled until it's fixed.
     runs-on: ${{ matrix.config.os }}

From 81d69908114e9ebaaaa034eb79ec762e3ee5bc44 Mon Sep 17 00:00:00 2001
From: Kelvin <26215587+zktuong@users.noreply.github.com>
Date: Thu, 21 Apr 2022 22:40:58 +0100
Subject: [PATCH 05/11] does this work?

---
 tests/test_preprocessing.py | 34 ++++++++++++++++++++--------------
 tests/test_rpy2.py          |  2 ++
 2 files changed, 22 insertions(+), 14 deletions(-)

diff --git a/tests/test_preprocessing.py b/tests/test_preprocessing.py
index acd7693ca..44e74fd37 100644
--- a/tests/test_preprocessing.py
+++ b/tests/test_preprocessing.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 import pytest
+import sys
 import os
 import pandas as pd
 import dandelion as ddl
@@ -8,12 +9,13 @@
 from fixtures import (fasta_10x, annotation_10x, create_testfolder,
                       database_paths, dummy_adata, processed_files)
 
-if 'IGDATA' in os.environ:
-    del os.environ["IGDATA"]
-if 'GERMLINE' in os.environ:
-    del os.environ["GERMLINE"]
-if 'GERMLINE' in os.environ:
-    del os.environ["GERMLINE"]
+try:
+    os.environ.pop('IGDATA')
+    os.environ.pop('GERMLINE')
+    os.environ.pop('BLASTDB')
+except:
+    pass
+
 
 @pytest.mark.parametrize("filename,expected",
                          [pytest.param('filtered', 1),
@@ -64,9 +66,10 @@ def test_reannotate_fails(create_testfolder, database_paths):
                                 filename_prefix='filtered')
 
 
-@pytest.mark.parametrize("filename,expected",
-                         [pytest.param('filtered', 5),
-                          pytest.param('all', 10)])
+@pytest.mark.parametrize(
+    "filename,expected",
+    [pytest.param('filtered', 5),
+     pytest.param('all', 10)])
 def test_reannotategenes(create_testfolder, database_paths, filename,
                          expected):
     ddl.pp.reannotate_genes(str(create_testfolder),
@@ -158,11 +161,13 @@ def test_update_germlines(create_testfolder, processed_files, database_paths):
     assert len(vdj.germline) > 0
 
 
-@pytest.mark.parametrize(
-    "freq,colname,dtype",
-    [pytest.param(True, 'mu_freq', float),
-     pytest.param(False, 'mu_count', int)])
-def test_quantify_mut(create_testfolder, processed_files, freq, colname, dtype):
+@pytest.mark.parametrize("freq,colname,dtype", [
+    pytest.param(True, 'mu_freq', float),
+    pytest.param(False, 'mu_count', int)
+])
+@pytest.mark.skipif(sys.platform == 'darwin')
+def test_quantify_mut(create_testfolder, processed_files, freq, colname,
+                      dtype):
     f = create_testfolder / str('dandelion/' + processed_files['filtered'])
     ddl.pp.quantify_mutations(f, frequency=freq)
     dat = pd.read_csv(f, sep='\t')
@@ -174,6 +179,7 @@ def test_quantify_mut(create_testfolder, processed_files, freq, colname, dtype):
     "freq,colname",
     [pytest.param(True, 'mu_freq'),
      pytest.param(False, 'mu_count')])
+@pytest.mark.skipif(sys.platform == 'darwin')
 def test_quantify_mut_2(create_testfolder, processed_files, freq, colname):
     f = create_testfolder / str('dandelion/' + processed_files['filtered'])
     vdj = ddl.Dandelion(f)
diff --git a/tests/test_rpy2.py b/tests/test_rpy2.py
index bcc85b111..cef9df712 100644
--- a/tests/test_rpy2.py
+++ b/tests/test_rpy2.py
@@ -15,6 +15,7 @@ def test_importrpy2():
     assert sh.__module__ == 'rpy2.robjects.packages'
 
 
+@pytest.mark.skipif(sys.platform == 'darwin')
 def test_mutation(create_testfolder, airr_reannotated):
     f = create_testfolder / "test.tsv"
     airr_reannotated.to_csv(f, sep='\t', index=False)
@@ -34,6 +35,7 @@ def test_create_germlines(create_testfolder, database_paths):
     assert not vdj.data.germline_alignment_d_mask.empty
 
 
+@pytest.mark.skipif(sys.platform == 'darwin')
 def test_manual_threshold_and_define_clones(create_testfolder):
     f = create_testfolder / "test.tsv"
     out = pd.read_csv(f, sep='\t')

From 1abd68371b2a2d3769bec6bda5e44c953f64b89e Mon Sep 17 00:00:00 2001
From: Kelvin <26215587+zktuong@users.noreply.github.com>
Date: Thu, 21 Apr 2022 22:47:57 +0100
Subject: [PATCH 06/11] oops

---
 tests/test_preprocessing.py | 4 ++--
 tests/test_rpy2.py          | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_preprocessing.py b/tests/test_preprocessing.py
index 44e74fd37..130c71b64 100644
--- a/tests/test_preprocessing.py
+++ b/tests/test_preprocessing.py
@@ -165,7 +165,7 @@ def test_update_germlines(create_testfolder, processed_files, database_paths):
     pytest.param(True, 'mu_freq', float),
     pytest.param(False, 'mu_count', int)
 ])
-@pytest.mark.skipif(sys.platform == 'darwin')
+@pytest.mark.skipif(sys.platform == 'darwin', reason="macos CI stalls.")
 def test_quantify_mut(create_testfolder, processed_files, freq, colname,
                       dtype):
     f = create_testfolder / str('dandelion/' + processed_files['filtered'])
@@ -179,7 +179,7 @@ def test_quantify_mut(create_testfolder, processed_files, freq, colname,
     "freq,colname",
     [pytest.param(True, 'mu_freq'),
      pytest.param(False, 'mu_count')])
-@pytest.mark.skipif(sys.platform == 'darwin')
+@pytest.mark.skipif(sys.platform == 'darwin', reason="macos CI stalls.")
 def test_quantify_mut_2(create_testfolder, processed_files, freq, colname):
     f = create_testfolder / str('dandelion/' + processed_files['filtered'])
     vdj = ddl.Dandelion(f)
diff --git a/tests/test_rpy2.py b/tests/test_rpy2.py
index cef9df712..1a317d285 100644
--- a/tests/test_rpy2.py
+++ b/tests/test_rpy2.py
@@ -15,7 +15,7 @@ def test_importrpy2():
     assert sh.__module__ == 'rpy2.robjects.packages'
 
 
-@pytest.mark.skipif(sys.platform == 'darwin')
+@pytest.mark.skipif(sys.platform == 'darwin', reason="macos CI stalls.")
 def test_mutation(create_testfolder, airr_reannotated):
     f = create_testfolder / "test.tsv"
     airr_reannotated.to_csv(f, sep='\t', index=False)
@@ -35,7 +35,7 @@ def test_create_germlines(create_testfolder, database_paths):
     assert not vdj.data.germline_alignment_d_mask.empty
 
 
-@pytest.mark.skipif(sys.platform == 'darwin')
+@pytest.mark.skipif(sys.platform == 'darwin', reason="macos CI stalls.")
 def test_manual_threshold_and_define_clones(create_testfolder):
     f = create_testfolder / "test.tsv"
     out = pd.read_csv(f, sep='\t')

From cb5116afd2a78df35f94e57bca7d515559df701e Mon Sep 17 00:00:00 2001
From: Kelvin <26215587+zktuong@users.noreply.github.com>
Date: Thu, 21 Apr 2022 22:53:38 +0100
Subject: [PATCH 07/11] Update test_rpy2.py

---
 tests/test_rpy2.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_rpy2.py b/tests/test_rpy2.py
index 1a317d285..805a4cb54 100644
--- a/tests/test_rpy2.py
+++ b/tests/test_rpy2.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 import pandas as pd
 import dandelion as ddl
+import pytest
 
 from fixtures import (airr_reannotated, create_testfolder, database_paths)
 

From 25d3cd9ef122fd5643008e96002e2ad0b54806df Mon Sep 17 00:00:00 2001
From: Kelvin <26215587+zktuong@users.noreply.github.com>
Date: Thu, 21 Apr 2022 23:06:39 +0100
Subject: [PATCH 08/11] Update test_rpy2.py

---
 tests/test_rpy2.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_rpy2.py b/tests/test_rpy2.py
index 805a4cb54..8d2a31003 100644
--- a/tests/test_rpy2.py
+++ b/tests/test_rpy2.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 import pandas as pd
 import dandelion as ddl
+import sys
 import pytest
 
 from fixtures import (airr_reannotated, create_testfolder, database_paths)

From ae81d979093834140da64275f024b5acd3b3bcce Mon Sep 17 00:00:00 2001
From: Kelvin <26215587+zktuong@users.noreply.github.com>
Date: Thu, 21 Apr 2022 23:46:43 +0100
Subject: [PATCH 09/11] Update test_rpy2.py

---
 tests/test_rpy2.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_rpy2.py b/tests/test_rpy2.py
index 8d2a31003..7cd68ce5a 100644
--- a/tests/test_rpy2.py
+++ b/tests/test_rpy2.py
@@ -7,6 +7,7 @@
 from fixtures import (airr_reannotated, create_testfolder, database_paths)
 
 
+@pytest.mark.skipif(sys.platform == 'darwin', reason="macos CI stalls.")
 def test_importrpy2():
 
     from rpy2.robjects.packages import importr

From 46df801bee2917e5eef2ae26bc9c8d3a1c8f1683 Mon Sep 17 00:00:00 2001
From: Kelvin <26215587+zktuong@users.noreply.github.com>
Date: Fri, 22 Apr 2022 06:09:56 +0100
Subject: [PATCH 10/11] Update test_rpy2.py

---
 tests/test_rpy2.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_rpy2.py b/tests/test_rpy2.py
index 7cd68ce5a..5fe9b93cf 100644
--- a/tests/test_rpy2.py
+++ b/tests/test_rpy2.py
@@ -30,6 +30,7 @@ def test_mutation(create_testfolder, airr_reannotated):
     assert not vdj.data.mu_freq.empty
 
 
+@pytest.mark.skipif(sys.platform == 'darwin', reason="macos CI stalls.")
 def test_create_germlines(create_testfolder, database_paths):
     f = create_testfolder / "test.tsv"
     out = pd.read_csv(f, sep='\t')

From 6e53c0ddb392682a811685354d62c9a83fbc7120 Mon Sep 17 00:00:00 2001
From: Kelvin <26215587+zktuong@users.noreply.github.com>
Date: Fri, 22 Apr 2022 08:52:14 +0100
Subject: [PATCH 11/11] Update tests.yml

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 2221a85d1..407b739d0 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -27,7 +27,7 @@ jobs:
           - { python-version: 3.9, os: ubuntu-latest }
           - { python-version: 3.7, os: macos-latest }
           - { python-version: 3.8, os: macos-latest }
-          # - { python-version: 3.9, os: macos-latest } # segmentation fault due to missing py3.9 macOSX wheel https://github.com/rpy2/rpy2/issues/846
+          - { python-version: 3.9, os: macos-latest } # segmentation fault due to missing py3.9 macOSX wheel https://github.com/rpy2/rpy2/issues/846
           # disabled until it's fixed.
     runs-on: ${{ matrix.config.os }}
     env: