From 47b846f57e8fd8ca65e03c1b4ebc8c57cff4992b Mon Sep 17 00:00:00 2001
From: Anil Thanki <thanki.anil@gmail.com>
Date: Fri, 5 Jul 2024 09:49:58 +0100
Subject: [PATCH 1/6] adding some int and empty values to metadata

---
 scanpy-scripts-tests.bats | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scanpy-scripts-tests.bats b/scanpy-scripts-tests.bats
index 93af736d..07b507c1 100755
--- a/scanpy-scripts-tests.bats
+++ b/scanpy-scripts-tests.bats
@@ -180,7 +180,7 @@ setup() {
         skip "$singlet_obs exists"
     fi
 
-    run rm -rf $batch_obs && echo -e "batch\n$(printf "%0.sbatch1\n" {1..1350})\n$(printf "%0.sbatch2\n" {1..1350})" > $batch_obs
+    run rm -rf $batch_obs && echo -e "batch\n$(printf "%0.sbatch1\n" {1..1350})\n$(printf "%0.sbatch2\n" {1..1350})" | awk '{if (NR == 1) {print $0; next} if (NR % 100 == 0) {print NR / 100; next} if (NR % 250 == 0) {print ""; next} print $0}' > $batch_obs
 
     [ "$status" -eq 0 ]
     [ -f "$batch_obs" ]

From 1ac810ddd96ff823fee02289e6a4d87db39002b9 Mon Sep 17 00:00:00 2001
From: Anil Thanki <thanki.anil@gmail.com>
Date: Thu, 22 Aug 2024 13:20:13 +0100
Subject: [PATCH 2/6] Update scanpy-scripts-tests.bats - adding additional
 column of mixed content

---
 scanpy-scripts-tests.bats | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scanpy-scripts-tests.bats b/scanpy-scripts-tests.bats
index 07b507c1..86e1d3f2 100755
--- a/scanpy-scripts-tests.bats
+++ b/scanpy-scripts-tests.bats
@@ -180,7 +180,7 @@ setup() {
         skip "$singlet_obs exists"
     fi
 
-    run rm -rf $batch_obs && echo -e "batch\n$(printf "%0.sbatch1\n" {1..1350})\n$(printf "%0.sbatch2\n" {1..1350})" | awk '{if (NR == 1) {print $0; next} if (NR % 100 == 0) {print NR / 100; next} if (NR % 250 == 0) {print ""; next} print $0}' > $batch_obs
+    run rm -rf $batch_obs && echo -e "batch\tadditional_column\n$(for i in {1..1350}; do echo -e "batch1\tdata$i"; done)\n$(for i in {1..1350}; do echo -e "batch2\tinfo$i"; done)" > $batch_obs
 
     [ "$status" -eq 0 ]
     [ -f "$batch_obs" ]

From 0be484be6926ff546b7a1d0974fcc912430e2505 Mon Sep 17 00:00:00 2001
From: Anil Thanki <thanki.anil@gmail.com>
Date: Thu, 22 Aug 2024 14:25:17 +0100
Subject: [PATCH 3/6] Update test-env.yaml -  updates anndata version

---
 test-env.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test-env.yaml b/test-env.yaml
index 83b06361..50a2cef5 100644
--- a/test-env.yaml
+++ b/test-env.yaml
@@ -5,6 +5,7 @@ channels:
   - defaults
 dependencies:
   - scanpy=1.9.3
+  - anndata=0.10.5.post1
   - louvain
   - igraph
   - leidenalg

From c2ea131b4e29230db9d2894df69bb127201b6849 Mon Sep 17 00:00:00 2001
From: Anil Thanki <thanki.anil@gmail.com>
Date: Thu, 22 Aug 2024 14:45:00 +0100
Subject: [PATCH 4/6] Update test-env.yaml - sets python version

---
 test-env.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test-env.yaml b/test-env.yaml
index 50a2cef5..5f7dfeab 100644
--- a/test-env.yaml
+++ b/test-env.yaml
@@ -4,6 +4,7 @@ channels:
   - bioconda
   - defaults
 dependencies:
+  - python=3.9.18
   - scanpy=1.9.3
   - anndata=0.10.5.post1
   - louvain

From 1d6462f93556bb2e6099fcba8187bf58ad586831 Mon Sep 17 00:00:00 2001
From: Anil Thanki <thanki.anil@gmail.com>
Date: Thu, 22 Aug 2024 15:12:53 +0100
Subject: [PATCH 5/6] Update python-package.yml - set python to 3.9

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

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 2e9db02f..9f6e5895 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9"]
+        python-version: ["3.9"]
 
     steps:
     - uses: actions/checkout@v2

From 3454d5d636e269f3ed6ad4c74c5fcf61b5838657 Mon Sep 17 00:00:00 2001
From: Anil Thanki <thanki.anil@gmail.com>
Date: Thu, 22 Aug 2024 16:05:35 +0100
Subject: [PATCH 6/6] Update test-env.yaml - update h5py

---
 test-env.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test-env.yaml b/test-env.yaml
index 5f7dfeab..cb39577d 100644
--- a/test-env.yaml
+++ b/test-env.yaml
@@ -6,6 +6,7 @@ channels:
 dependencies:
   - python=3.9.18
   - scanpy=1.9.3
+  - h5py=3.10.0
   - anndata=0.10.5.post1
   - louvain
   - igraph