From 535bff60de688188302e5e021e62c2c4e6f7dbae Mon Sep 17 00:00:00 2001
From: Misha Mikhasenko <mikhail.mikhasenko@gmail.com>
Date: Fri, 26 Aug 2022 14:38:46 +0200
Subject: [PATCH 1/6] add python env

---
 environment.yml | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 environment.yml

diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..aaf9f64
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,10 @@
+name: mol2net
+channels:
+- conda-forge
+dependencies:
+- python>=3.6
+- pandas
+- numpy
+- scipy
+- scipy
+- matplotlib

From 2f33106d07d317413b1f3c78cf350fca5afa5035 Mon Sep 17 00:00:00 2001
From: Misha Mikhasenko <mikhail.mikhasenko@gmail.com>
Date: Fri, 26 Aug 2022 14:45:38 +0200
Subject: [PATCH 2/6] Create python-package-conda.yml

---
 .github/workflows/python-package-conda.yml | 23 ++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 .github/workflows/python-package-conda.yml

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
new file mode 100644
index 0000000..ef1f328
--- /dev/null
+++ b/.github/workflows/python-package-conda.yml
@@ -0,0 +1,23 @@
+name: Python Package using Conda
+
+on: [push]
+
+jobs:
+  run-code:
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.10
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env create
+        conda run -n mol2net python 1_2_mol2net.py
+        conda run -n mol2net python 3_netAna.py

From 676ebe551ce07fce67be204497f52f051ae4a768 Mon Sep 17 00:00:00 2001
From: Misha Mikhasenko <mikhail.mikhasenko@gmail.com>
Date: Fri, 26 Aug 2022 15:01:30 +0200
Subject: [PATCH 3/6] remove python step in ci

---
 .github/workflows/python-package-conda.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index ef1f328..6d3037f 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -8,10 +8,6 @@ jobs:
     
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
-      with:
-        python-version: 3.10
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory

From 3e0ba4788599e5805d60a8462f7ece0585794ce5 Mon Sep 17 00:00:00 2001
From: rufalexan <112173397+rufalexan@users.noreply.github.com>
Date: Mon, 19 Sep 2022 13:25:15 +0200
Subject: [PATCH 4/6] revisit deps

---
 environment.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index aaf9f64..ee75c57 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,9 +2,9 @@ name: mol2net
 channels:
 - conda-forge
 dependencies:
-- python>=3.6
+- python=3.10.4
 - pandas
+- networkx
 - numpy
 - scipy
-- scipy
 - matplotlib

From 0602db1b6993fd1dc442f667c1d24fd2945afa38 Mon Sep 17 00:00:00 2001
From: rufalexan <112173397+rufalexan@users.noreply.github.com>
Date: Mon, 19 Sep 2022 13:30:24 +0200
Subject: [PATCH 5/6] fix scipy version

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index ee75c57..006856e 100644
--- a/environment.yml
+++ b/environment.yml
@@ -6,5 +6,5 @@ dependencies:
 - pandas
 - networkx
 - numpy
-- scipy
+- scipy=1.8.1
 - matplotlib

From 175ff92d838e013688cb60de7d06e226be08051c Mon Sep 17 00:00:00 2001
From: rufalexan <112173397+rufalexan@users.noreply.github.com>
Date: Mon, 19 Sep 2022 13:33:07 +0200
Subject: [PATCH 6/6] modified pipeline

---
 .github/workflows/python-package-conda.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 6d3037f..b945b5e 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -15,5 +15,4 @@ jobs:
     - name: Install dependencies
       run: |
         conda env create
-        conda run -n mol2net python 1_2_mol2net.py
-        conda run -n mol2net python 3_netAna.py
+        conda run -n mol2net sh mol2net.sh