From b3deba255d228cf8b3d45871887c289c6c7a4f9a Mon Sep 17 00:00:00 2001
From: Karen Loaiza <kloc@ssi.dk>
Date: Fri, 25 Aug 2023 15:38:11 +0200
Subject: [PATCH 1/3] Create workflow to solve conda env

---
 .github/workflows/solve_conda_env.yml | 28 +++++++++++++++++++++++++++
 environment.yml                       |  9 +++++----
 2 files changed, 33 insertions(+), 4 deletions(-)
 create mode 100644 .github/workflows/solve_conda_env.yml

diff --git a/.github/workflows/solve_conda_env.yml b/.github/workflows/solve_conda_env.yml
new file mode 100644
index 0000000..ef8cfd1
--- /dev/null
+++ b/.github/workflows/solve_conda_env.yml
@@ -0,0 +1,28 @@
+name: Solve conda environment
+
+on: [push]
+
+jobs:
+  check-conda:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout Code
+      uses: actions/checkout@v2
+
+    - name: Set up Miniconda
+      uses: conda-incubator/setup-miniconda@v2
+
+    - name: Install conda dependencies
+      run: |
+        $CONDA/bin/conda env update --file environment.yml --name base
+
+    - name: Format with black
+      run: |
+        $CONDA/bin/black *.py
+        $CONDA/bin/black */*.py
+
+    - name: Check conda dependencies are compatible with the main program
+      run: |
+        $CONDA/bin/python --version
+        $CONDA/bin/chewBBACA.py -h
diff --git a/environment.yml b/environment.yml
index 5e2e668..15b02fc 100755
--- a/environment.yml
+++ b/environment.yml
@@ -3,10 +3,10 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - snakemake-minimal==5.31.1 # updated from 5.7.1 because of envvars
-  - blast==2.14.0 # updated from blast>=2.9
-  - prodigal==2.6.3
-  - chewbbaca==3.2.0
+  - snakemake-minimal>=5.31.1 # updated from 5.7.1 because of envvars
+  - blast>=2.14.0 # updated from blast>=2.9
+  - prodigal>=2.6.3
+  - chewbbaca>=3.2.0
   - pip
   - pip:
     - pytest
@@ -17,4 +17,5 @@ dependencies:
     - argh
     - watchdog
     - bifrostlib
+    - black
     - -e .

From b9123ca902ff86e4b34d2636b0bfad9c16391372 Mon Sep 17 00:00:00 2001
From: Karen <47039819+kalilamali@users.noreply.github.com>
Date: Fri, 25 Aug 2023 23:21:31 +0200
Subject: [PATCH 2/3] Update solve_conda_env.yml to generalize to all bifrost
 repos

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

diff --git a/.github/workflows/solve_conda_env.yml b/.github/workflows/solve_conda_env.yml
index ef8cfd1..fe9a118 100644
--- a/.github/workflows/solve_conda_env.yml
+++ b/.github/workflows/solve_conda_env.yml
@@ -25,4 +25,4 @@ jobs:
     - name: Check conda dependencies are compatible with the main program
       run: |
         $CONDA/bin/python --version
-        $CONDA/bin/chewBBACA.py -h
+  

From bdf3cdc174a6234277e8e9fb33fc18ab29438d94 Mon Sep 17 00:00:00 2001
From: Kristoffer Kiil <kriskiil@users.noreply.github.com>
Date: Thu, 5 Oct 2023 09:30:56 +0200
Subject: [PATCH 3/3] Update config.yaml

lowercased display name
---
 bifrost_chewbbaca/config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bifrost_chewbbaca/config.yaml b/bifrost_chewbbaca/config.yaml
index 4d88198..f524a92 100755
--- a/bifrost_chewbbaca/config.yaml
+++ b/bifrost_chewbbaca/config.yaml
@@ -1,5 +1,5 @@
 #-Basic info----------------------------------------------------------------------------------------
-display_name: chewBBACA
+display_name: chewbbaca
 name: chewbbaca__v1.0.6
 version:
   schema: ["v2_1_0"]