From d6c1af10415b28ed9d93d70f6ae680e40ec8c0de Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Mon, 7 Oct 2024 12:08:34 +0100
Subject: [PATCH 01/14] Update approve-trigger.yml

---
 .github/workflows/approve-trigger.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/approve-trigger.yml b/.github/workflows/approve-trigger.yml
index 1ac292e33..c93c23cb4 100644
--- a/.github/workflows/approve-trigger.yml
+++ b/.github/workflows/approve-trigger.yml
@@ -7,6 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Approve Command Trigger
+        if: contains(toJson(github.event.issue.labels), 'Model Request') 
         uses: peter-evans/slash-command-dispatch@13bc09769d122a64f75aa5037256f6f2d78be8c4 # pin@v4.0.0
         with:
           token: ${{ secrets.PAT }}

From a3823c8c966ba72abfdaabb96b73fd5d750a771f Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Mon, 7 Oct 2024 15:19:11 +0100
Subject: [PATCH 02/14] Update approve-trigger.yml

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

diff --git a/.github/workflows/approve-trigger.yml b/.github/workflows/approve-trigger.yml
index c93c23cb4..49fa4bdb2 100644
--- a/.github/workflows/approve-trigger.yml
+++ b/.github/workflows/approve-trigger.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Approve Command Trigger
-        if: contains(toJson(github.event.issue.labels), 'Model Request') 
+        if: contains(github.event.issue.labels.*.name, 'Model Request') 
         uses: peter-evans/slash-command-dispatch@13bc09769d122a64f75aa5037256f6f2d78be8c4 # pin@v4.0.0
         with:
           token: ${{ secrets.PAT }}

From 20470335065bf1c4271fe0a8f21dbad3936da243 Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Mon, 7 Oct 2024 15:35:38 +0100
Subject: [PATCH 03/14] Newly Updated approve-trigger.yml

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

diff --git a/.github/workflows/approve-trigger.yml b/.github/workflows/approve-trigger.yml
index 49fa4bdb2..814f4b09b 100644
--- a/.github/workflows/approve-trigger.yml
+++ b/.github/workflows/approve-trigger.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Approve Command Trigger
-        if: contains(github.event.issue.labels.*.name, 'Model Request') 
+        if: contains(github.event.issue.labels.*.name, 'Model Request')
         uses: peter-evans/slash-command-dispatch@13bc09769d122a64f75aa5037256f6f2d78be8c4 # pin@v4.0.0
         with:
           token: ${{ secrets.PAT }}

From 1ebe594d858f780c7b04ee0dce10c21b24289cf8 Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Mon, 7 Oct 2024 16:18:17 +0100
Subject: [PATCH 04/14] Update approve-trigger.yml


From 13b9de654ec5741aaf2e434b4b1c3cb31ca90d0a Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Mon, 7 Oct 2024 16:53:34 +0100
Subject: [PATCH 05/14] Update approve-trigger.yml

---
 .github/workflows/approve-trigger.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/approve-trigger.yml b/.github/workflows/approve-trigger.yml
index 814f4b09b..76bf5f70a 100644
--- a/.github/workflows/approve-trigger.yml
+++ b/.github/workflows/approve-trigger.yml
@@ -2,10 +2,14 @@ name: Approve Command Trigger
 on:
   issue_comment:
     types: [created]
+
 jobs:
   approve-command-trigger:
     runs-on: ubuntu-latest
     steps:
+      - name: Log: Checking for 'Model Request' label
+        run: echo "Checking if the 'Model Request' label is present on the issue"
+
       - name: Approve Command Trigger
         if: contains(github.event.issue.labels.*.name, 'Model Request')
         uses: peter-evans/slash-command-dispatch@13bc09769d122a64f75aa5037256f6f2d78be8c4 # pin@v4.0.0
@@ -16,3 +20,6 @@ jobs:
           reactions: false
           commands: |
             approve
+
+      - name: Log: Approval process completed
+        run: echo "Approval process has been completed."

From aed976eeb52d552f7efff30f41ab4da867107b66 Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Mon, 7 Oct 2024 18:00:47 +0100
Subject: [PATCH 06/14] Update approve-trigger.yml

---
 .github/workflows/approve-trigger.yml | 29 ++++++++++++++-------------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/approve-trigger.yml b/.github/workflows/approve-trigger.yml
index 76bf5f70a..4e5ef9751 100644
--- a/.github/workflows/approve-trigger.yml
+++ b/.github/workflows/approve-trigger.yml
@@ -7,19 +7,20 @@ jobs:
   approve-command-trigger:
     runs-on: ubuntu-latest
     steps:
-      - name: Log: Checking for 'Model Request' label
-        run: echo "Checking if the 'Model Request' label is present on the issue"
+    - name: Log Checking for 'Model Request' label
+      run: echo "Checking if the 'Model Request' label is present on the issue"
 
-      - name: Approve Command Trigger
-        if: contains(github.event.issue.labels.*.name, 'Model Request')
-        uses: peter-evans/slash-command-dispatch@13bc09769d122a64f75aa5037256f6f2d78be8c4 # pin@v4.0.0
-        with:
-          token: ${{ secrets.PAT }}
-          issue-type: issue
-          permission: write
-          reactions: false
-          commands: |
-            approve
+    - name: Approve Command Trigger
+      if: contains(github.event.issue.labels.*.name, 'Model Request')
+      uses: peter-evans/slash-command-dispatch@13bc09769d122a64f75aa5037256f6f2d78be8c4 # pin@v4.0.0
+      with:
+        token: ${{ secrets.PAT }}
+        issue-type: issue
+        permission: write
+        reactions: false
+        commands: |
+          approve
+
+    - name: Log Approval process completed
+      run: echo "Approval process has been completed."
 
-      - name: Log: Approval process completed
-        run: echo "Approval process has been completed."

From a3a5257504647a0717f3f8b37ad7ffbff4e7c527 Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Wed, 9 Oct 2024 17:49:19 +0100
Subject: [PATCH 07/14] Update approve-trigger.yml

I have removed the steps that log messages related to the approval process and label checking. The workflow now triggers the approval command when the 'Model Request' label is detected, streamlining the process by eliminating log outputs.
---
 .github/workflows/approve-trigger.yml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/.github/workflows/approve-trigger.yml b/.github/workflows/approve-trigger.yml
index 4e5ef9751..7eee372b4 100644
--- a/.github/workflows/approve-trigger.yml
+++ b/.github/workflows/approve-trigger.yml
@@ -7,9 +7,6 @@ jobs:
   approve-command-trigger:
     runs-on: ubuntu-latest
     steps:
-    - name: Log Checking for 'Model Request' label
-      run: echo "Checking if the 'Model Request' label is present on the issue"
-
     - name: Approve Command Trigger
       if: contains(github.event.issue.labels.*.name, 'Model Request')
       uses: peter-evans/slash-command-dispatch@13bc09769d122a64f75aa5037256f6f2d78be8c4 # pin@v4.0.0
@@ -20,7 +17,3 @@ jobs:
         reactions: false
         commands: |
           approve
-
-    - name: Log Approval process completed
-      run: echo "Approval process has been completed."
-

From 81a38b5593eedfebe9893870fb1e1c61a7129ef4 Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Wed, 9 Oct 2024 17:54:51 +0100
Subject: [PATCH 08/14] Update approve-trigger.yml

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

diff --git a/.github/workflows/approve-trigger.yml b/.github/workflows/approve-trigger.yml
index 7eee372b4..c75a0e8df 100644
--- a/.github/workflows/approve-trigger.yml
+++ b/.github/workflows/approve-trigger.yml
@@ -5,10 +5,10 @@ on:
 
 jobs:
   approve-command-trigger:
+    if: contains(github.event.issue.labels.*.name, 'Model Request')
     runs-on: ubuntu-latest
     steps:
     - name: Approve Command Trigger
-      if: contains(github.event.issue.labels.*.name, 'Model Request')
       uses: peter-evans/slash-command-dispatch@13bc09769d122a64f75aa5037256f6f2d78be8c4 # pin@v4.0.0
       with:
         token: ${{ secrets.PAT }}

From ab9b3080c7708ee33030240534f5e008d3ac9a7a Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Thu, 10 Oct 2024 16:20:25 +0100
Subject: [PATCH 09/14] Update approve-trigger.yml

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

diff --git a/.github/workflows/approve-trigger.yml b/.github/workflows/approve-trigger.yml
index c75a0e8df..a43915fb0 100644
--- a/.github/workflows/approve-trigger.yml
+++ b/.github/workflows/approve-trigger.yml
@@ -5,7 +5,7 @@ on:
 
 jobs:
   approve-command-trigger:
-    if: contains(github.event.issue.labels.*.name, 'Model Request')
+    if: contains(github.event.issue.labels.*.name, 'new-model')
     runs-on: ubuntu-latest
     steps:
     - name: Approve Command Trigger

From 5c312b2a4c7fb7aee3d308790cda1ee576e69677 Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Sun, 13 Oct 2024 22:06:56 +0100
Subject: [PATCH 10/14] Update approve-trigger.yml

Indentation has been restored
---
 .github/workflows/approve-trigger.yml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/approve-trigger.yml b/.github/workflows/approve-trigger.yml
index a43915fb0..07d768719 100644
--- a/.github/workflows/approve-trigger.yml
+++ b/.github/workflows/approve-trigger.yml
@@ -8,12 +8,12 @@ jobs:
     if: contains(github.event.issue.labels.*.name, 'new-model')
     runs-on: ubuntu-latest
     steps:
-    - name: Approve Command Trigger
-      uses: peter-evans/slash-command-dispatch@13bc09769d122a64f75aa5037256f6f2d78be8c4 # pin@v4.0.0
-      with:
-        token: ${{ secrets.PAT }}
-        issue-type: issue
-        permission: write
-        reactions: false
-        commands: |
-          approve
+      - name: Approve Command Trigger
+        uses: peter-evans/slash-command-dispatch@13bc09769d122a64f75aa5037256f6f2d78be8c4 # pin@v4.0.0
+        with:
+          token: ${{ secrets.PAT }}
+          issue-type: issue
+          permission: write
+          reactions: false
+          commands: |
+            approve

From a1fe79028fce5f2e4e7771b9ddf5fb8aaaa58daa Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Mon, 14 Oct 2024 17:18:45 +0100
Subject: [PATCH 11/14] Update pr_check.yml

---
 .github/workflows/pr_check.yml | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
index abd2253e4..76a1d1ce0 100644
--- a/.github/workflows/pr_check.yml
+++ b/.github/workflows/pr_check.yml
@@ -17,15 +17,15 @@ jobs:
     steps:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # pin@v3.5.3
 
-      - name: Add conda to system path
-        run: echo $CONDA/bin >> $GITHUB_PATH
+      - name: Install Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: 3.10  
+      - name: Create and activate Conda environment
+        run: |
+          conda create --name ersilia-env python=3.10.10 -y
+          conda activate ersilia-env
 
-      - name: Set Python to 3.10.10
-        run:
-         conda install -y python=3.10.10 
-      
-      - name: Source conda
-        run: source $CONDA/etc/profile.d/conda.sh
 
       - name: Install dependencies
         run: |
@@ -79,4 +79,5 @@ jobs:
 
       - name: Local catalog
         run: |
+          conda activate ersilia-env
           ersilia catalog --local

From 8c2e65c06ae7dc4a5796a575efe6ae8df0ddd464 Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Mon, 14 Oct 2024 17:45:55 +0100
Subject: [PATCH 12/14] Update pr_check.yml

---
 .github/workflows/pr_check.yml | 48 ++++++++++++++--------------------
 1 file changed, 19 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
index 76a1d1ce0..0a73f3c19 100644
--- a/.github/workflows/pr_check.yml
+++ b/.github/workflows/pr_check.yml
@@ -5,7 +5,6 @@ on:
     branches: [ master ]
   push:
     branches: [ master ]
-
   workflow_dispatch:
 
 permissions:
@@ -15,43 +14,33 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # pin@v3.5.3
-
+      - uses: actions/checkout@v3
+      
       - name: Install Miniconda
         uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: 3.10  
+          python-version: 3.10
+
       - name: Create and activate Conda environment
         run: |
           conda create --name ersilia-env python=3.10.10 -y
+          source $CONDA/etc/profile.d/conda.sh
           conda activate ersilia-env
-
-
+          
       - name: Install dependencies
         run: |
-          source activate
-          conda init
-          conda install git-lfs -c conda-forge
-          git-lfs install
-          conda install gh -c conda-forge
-
-      - name: Install Ersilia
-        run: |
-          source activate
-          python --version
-          echo "After conda init"
-          conda init
-          python -m pip install -e .[test]
-
-      - name: Hub catalog
-        run: |
-          ersilia catalog
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate ersilia-env
+          conda init  
+          conda install git-lfs gh -c conda-forge -y  # Install git-lfs and gh
+          git-lfs install 
+          python -m pip install -e .
 
       - name: Fetch model from GitHub
         run: |
-          source activate
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate ersilia-env
           ersilia -v fetch molecular-weight --from_github
-          echo "Serving molecular-weight model."
           ersilia serve molecular-weight
           ersilia info
           ersilia run -i "CC(=O)OC1=CC=CC=C1C(=O)O" | grep "180.15899"
@@ -59,9 +48,9 @@ jobs:
 
       - name: Fetch model from S3
         run: |
-          source activate
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate ersilia-env
           ersilia -v fetch molecular-weight --from_s3
-          echo "Serving molecular-weight model."
           ersilia serve molecular-weight
           ersilia info
           ersilia run -i "CC(=O)OC1=CC=CC=C1C(=O)O" | grep "180.15899"
@@ -69,9 +58,9 @@ jobs:
 
       - name: Fetch model from DockerHub
         run: |
-          source activate
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate ersilia-env
           ersilia -v fetch molecular-weight --from_dockerhub
-          echo "Serving molecular-weight model."
           ersilia serve molecular-weight
           ersilia info
           ersilia run -i "CC(=O)OC1=CC=CC=C1C(=O)O" | grep "180.15899"
@@ -79,5 +68,6 @@ jobs:
 
       - name: Local catalog
         run: |
+          source $CONDA/etc/profile.d/conda.sh
           conda activate ersilia-env
           ersilia catalog --local

From 9051c350104142e4efaf9018d98dfbd09a761c85 Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Mon, 14 Oct 2024 18:25:49 +0100
Subject: [PATCH 13/14] Update pr_check.yml

---
 .github/workflows/pr_check.yml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
index 0a73f3c19..26c8e1382 100644
--- a/.github/workflows/pr_check.yml
+++ b/.github/workflows/pr_check.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      
+
       - name: Install Miniconda
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -24,20 +24,21 @@ jobs:
       - name: Create and activate Conda environment
         run: |
           conda create --name ersilia-env python=3.10.10 -y
-          source $CONDA/etc/profile.d/conda.sh
+          echo "source $CONDA/etc/profile.d/conda.sh" >> ~/.bashrc
+          source ~/.bashrc
           conda activate ersilia-env
-          
+
       - name: Install dependencies
         run: |
           source $CONDA/etc/profile.d/conda.sh
           conda activate ersilia-env
-          conda init  
-          conda install git-lfs gh -c conda-forge -y  # Install git-lfs and gh
-          git-lfs install 
+          conda install git-lfs gh -c conda-forge -y
+          git-lfs install
           python -m pip install -e .
 
       - name: Fetch model from GitHub
         run: |
+          set -euxo pipefail
           source $CONDA/etc/profile.d/conda.sh
           conda activate ersilia-env
           ersilia -v fetch molecular-weight --from_github

From 6aace2c79a6d6c5e5b42e34b6aa37317be30137c Mon Sep 17 00:00:00 2001
From: Aderemi Oluwadamilola <135835586+aderemi1224@users.noreply.github.com>
Date: Mon, 14 Oct 2024 18:31:36 +0100
Subject: [PATCH 14/14] Update pr_check.yml

---
 .github/workflows/pr_check.yml | 56 +++++++++++++++++++---------------
 1 file changed, 32 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
index 26c8e1382..abd2253e4 100644
--- a/.github/workflows/pr_check.yml
+++ b/.github/workflows/pr_check.yml
@@ -5,6 +5,7 @@ on:
     branches: [ master ]
   push:
     branches: [ master ]
+
   workflow_dispatch:
 
 permissions:
@@ -14,34 +15,43 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # pin@v3.5.3
 
-      - name: Install Miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          python-version: 3.10
+      - name: Add conda to system path
+        run: echo $CONDA/bin >> $GITHUB_PATH
 
-      - name: Create and activate Conda environment
-        run: |
-          conda create --name ersilia-env python=3.10.10 -y
-          echo "source $CONDA/etc/profile.d/conda.sh" >> ~/.bashrc
-          source ~/.bashrc
-          conda activate ersilia-env
+      - name: Set Python to 3.10.10
+        run:
+         conda install -y python=3.10.10 
+      
+      - name: Source conda
+        run: source $CONDA/etc/profile.d/conda.sh
 
       - name: Install dependencies
         run: |
-          source $CONDA/etc/profile.d/conda.sh
-          conda activate ersilia-env
-          conda install git-lfs gh -c conda-forge -y
+          source activate
+          conda init
+          conda install git-lfs -c conda-forge
           git-lfs install
-          python -m pip install -e .
+          conda install gh -c conda-forge
+
+      - name: Install Ersilia
+        run: |
+          source activate
+          python --version
+          echo "After conda init"
+          conda init
+          python -m pip install -e .[test]
+
+      - name: Hub catalog
+        run: |
+          ersilia catalog
 
       - name: Fetch model from GitHub
         run: |
-          set -euxo pipefail
-          source $CONDA/etc/profile.d/conda.sh
-          conda activate ersilia-env
+          source activate
           ersilia -v fetch molecular-weight --from_github
+          echo "Serving molecular-weight model."
           ersilia serve molecular-weight
           ersilia info
           ersilia run -i "CC(=O)OC1=CC=CC=C1C(=O)O" | grep "180.15899"
@@ -49,9 +59,9 @@ jobs:
 
       - name: Fetch model from S3
         run: |
-          source $CONDA/etc/profile.d/conda.sh
-          conda activate ersilia-env
+          source activate
           ersilia -v fetch molecular-weight --from_s3
+          echo "Serving molecular-weight model."
           ersilia serve molecular-weight
           ersilia info
           ersilia run -i "CC(=O)OC1=CC=CC=C1C(=O)O" | grep "180.15899"
@@ -59,9 +69,9 @@ jobs:
 
       - name: Fetch model from DockerHub
         run: |
-          source $CONDA/etc/profile.d/conda.sh
-          conda activate ersilia-env
+          source activate
           ersilia -v fetch molecular-weight --from_dockerhub
+          echo "Serving molecular-weight model."
           ersilia serve molecular-weight
           ersilia info
           ersilia run -i "CC(=O)OC1=CC=CC=C1C(=O)O" | grep "180.15899"
@@ -69,6 +79,4 @@ jobs:
 
       - name: Local catalog
         run: |
-          source $CONDA/etc/profile.d/conda.sh
-          conda activate ersilia-env
           ersilia catalog --local