From 0e0d13d67978325f2fccceda4233ec2f0b0fd07c Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 16:50:22 +1100
Subject: [PATCH 01/32] try get initial tests working

---
 .github/workflows/test.yaml                 | 45 +++++++++++++++++++++
 argos/argos_viewer/tests.py                 |  7 ++++
 devtools/conda-envs/argos-ubuntu-latest.yml | 11 +++--
 devtools/deployment/.env.example            |  2 +-
 4 files changed, 61 insertions(+), 4 deletions(-)
 create mode 100644 .github/workflows/test.yaml

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
new file mode 100644
index 0000000..970ab17
--- /dev/null
+++ b/.github/workflows/test.yaml
@@ -0,0 +1,45 @@
+name: ci
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    # Nightly tests run on main by default:
+    #   Scheduled workflows run on the latest commit on the default or base branch.
+    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+    - cron: "0 0 * * *"
+  workflow_dispatch:
+  merge_group:
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Install Docker Compose
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y docker-compose
+
+    - name: Build and run Docker Compose
+      run: |
+         docker-compose -f docker-compose-dev.yml up -d
+    - name: run tests
+      run: |
+         docker-compose -f docker-compose-dev.yml exec  web bash -c " cd argos &&  /opt/conda/bin/python  manage.py test"
\ No newline at end of file
diff --git a/argos/argos_viewer/tests.py b/argos/argos_viewer/tests.py
index 7ce503c..be7ee9d 100644
--- a/argos/argos_viewer/tests.py
+++ b/argos/argos_viewer/tests.py
@@ -1,3 +1,10 @@
 from django.test import TestCase
 
 # Create your tests here.
+
+class BlankTest(TestCase):
+    def test_placeholder(self):
+        self.assertEqual(1, 1)
+
+    def test_fail(self):
+        self.assertEqual(1,2)
diff --git a/devtools/conda-envs/argos-ubuntu-latest.yml b/devtools/conda-envs/argos-ubuntu-latest.yml
index 4ac5d49..7e3387d 100644
--- a/devtools/conda-envs/argos-ubuntu-latest.yml
+++ b/devtools/conda-envs/argos-ubuntu-latest.yml
@@ -6,12 +6,18 @@ dependencies:
 
   # Base depends
   - pip
-  - python =3.10
-  - git
+  - python >=3.10,<3.11
+
 
   # argos deps
   - django
   - gunicorn
+
+  # Testing
+  - pytest
+  - pytest-cov
+
+
   # asapdiscovery deps
 
   # Others
@@ -19,7 +25,6 @@ dependencies:
   - openeye-toolkits
   - pydantic >=1.10.8,<2.0.0a0
 
-
   # data
   - requests
   - boto3
diff --git a/devtools/deployment/.env.example b/devtools/deployment/.env.example
index 9b13331..f0222d3 100644
--- a/devtools/deployment/.env.example
+++ b/devtools/deployment/.env.example
@@ -5,4 +5,4 @@ DATABASE_URL=postgresql://django_traefik:django_traefik@db:5432/django_traefik
 HOST_DOMAIN=localhost
 POSTGRES_USER=django_traefik
 POSTGRES_PASSWORD=django_traefik
-POSTGRES_DB=django_traefik
+POSTGRES_DB=django_traefik
\ No newline at end of file

From b20382aee9759077b88866d60c307ceb5560d0f6 Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 16:53:19 +1100
Subject: [PATCH 02/32] add in env file

---
 .github/workflows/test.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 970ab17..3022e3d 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -36,6 +36,10 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get install -y docker-compose
+    
+    - name: copy example env file
+      run: |
+        cp devtools/deployment/.env.example .env
 
     - name: Build and run Docker Compose
       run: |

From c0d67fb915f87cd517c6711a023c3196082ce41c Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 16:55:52 +1100
Subject: [PATCH 03/32] fix names and rename file

---
 .github/workflows/{test.yaml => ci.yaml} | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)
 rename .github/workflows/{test.yaml => ci.yaml} (88%)

diff --git a/.github/workflows/test.yaml b/.github/workflows/ci.yaml
similarity index 88%
rename from .github/workflows/test.yaml
rename to .github/workflows/ci.yaml
index 3022e3d..bea8b71 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/ci.yaml
@@ -32,18 +32,18 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v2
 
-    - name: Install Docker Compose
+    - name: Install docker-compose
       run: |
         sudo apt-get update
         sudo apt-get install -y docker-compose
     
-    - name: copy example env file
+    - name: Copy example env file
       run: |
         cp devtools/deployment/.env.example .env
 
-    - name: Build and run Docker Compose
+    - name: Build and run containers
       run: |
          docker-compose -f docker-compose-dev.yml up -d
-    - name: run tests
+    - name: Run tests
       run: |
          docker-compose -f docker-compose-dev.yml exec  web bash -c " cd argos &&  /opt/conda/bin/python  manage.py test"
\ No newline at end of file

From c5a819cf6a5d25b4ed1ac2fb7511595489509c56 Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:00:44 +1100
Subject: [PATCH 04/32] fix

---
 .github/workflows/test.yaml | 67 +++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 .github/workflows/test.yaml

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
new file mode 100644
index 0000000..924e23b
--- /dev/null
+++ b/.github/workflows/test.yaml
@@ -0,0 +1,67 @@
+name: ci
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    # Nightly tests run on main by default:
+    #   Scheduled workflows run on the latest commit on the default or base branch.
+    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+    - cron: "0 0 * * *"
+  workflow_dispatch:
+  merge_group:
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+    
+
+jobs:
+
+  env:
+    OE_LICENSE: ${{ github.workspace }}/.OpenEye/oe_license.txt
+
+
+
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Install docker-compose
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y docker-compose
+    
+    - name: Copy example env file
+      run: |
+        cp devtools/deployment/.env.example .env
+
+    - name: Make .OpenEye directory
+      run: |
+        mkdir -p ${{ github.workspace }}/.OpenEye
+
+    - name: Test OE License & Write License to File
+      env:
+        OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
+      run: |
+        echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
+        python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'"
+
+
+    - name: Build and run containers
+      run: |
+         docker-compose -f docker-compose-dev.yml up -d
+    - name: Run tests
+      run: |
+         docker-compose -f docker-compose-dev.yml exec  web bash -c " cd argos &&  /opt/conda/bin/python  manage.py test"
\ No newline at end of file

From b17c64463288242e59538bbaa8639e8f16b4fc36 Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:02:04 +1100
Subject: [PATCH 05/32] fix again

---
 .github/workflows/test.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 924e23b..31807f6 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -51,6 +51,7 @@ jobs:
       run: |
         mkdir -p ${{ github.workspace }}/.OpenEye
 
+
     - name: Test OE License & Write License to File
       env:
         OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}

From 73a9418e26c5605f218ea5dca4839c6da3130cea Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:04:05 +1100
Subject: [PATCH 06/32] move to ci file

---
 .github/workflows/ci.yaml   | 21 +++++++++++-
 .github/workflows/test.yaml | 68 -------------------------------------
 2 files changed, 20 insertions(+), 69 deletions(-)
 delete mode 100644 .github/workflows/test.yaml

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index bea8b71..31807f6 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -22,9 +22,15 @@ concurrency:
 defaults:
   run:
     shell: bash -l {0}
-
+    
 
 jobs:
+
+  env:
+    OE_LICENSE: ${{ github.workspace }}/.OpenEye/oe_license.txt
+
+
+
   build:
     runs-on: ubuntu-latest
 
@@ -41,6 +47,19 @@ jobs:
       run: |
         cp devtools/deployment/.env.example .env
 
+    - name: Make .OpenEye directory
+      run: |
+        mkdir -p ${{ github.workspace }}/.OpenEye
+
+
+    - name: Test OE License & Write License to File
+      env:
+        OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
+      run: |
+        echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
+        python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'"
+
+
     - name: Build and run containers
       run: |
          docker-compose -f docker-compose-dev.yml up -d
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
deleted file mode 100644
index 31807f6..0000000
--- a/.github/workflows/test.yaml
+++ /dev/null
@@ -1,68 +0,0 @@
-name: ci
-
-on:
-  push:
-    branches:
-      - "main"
-  pull_request:
-    branches:
-      - "main"
-  schedule:
-    # Nightly tests run on main by default:
-    #   Scheduled workflows run on the latest commit on the default or base branch.
-    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
-    - cron: "0 0 * * *"
-  workflow_dispatch:
-  merge_group:
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.ref }}"
-  cancel-in-progress: true
-
-defaults:
-  run:
-    shell: bash -l {0}
-    
-
-jobs:
-
-  env:
-    OE_LICENSE: ${{ github.workspace }}/.OpenEye/oe_license.txt
-
-
-
-  build:
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Checkout code
-      uses: actions/checkout@v2
-
-    - name: Install docker-compose
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y docker-compose
-    
-    - name: Copy example env file
-      run: |
-        cp devtools/deployment/.env.example .env
-
-    - name: Make .OpenEye directory
-      run: |
-        mkdir -p ${{ github.workspace }}/.OpenEye
-
-
-    - name: Test OE License & Write License to File
-      env:
-        OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
-      run: |
-        echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
-        python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'"
-
-
-    - name: Build and run containers
-      run: |
-         docker-compose -f docker-compose-dev.yml up -d
-    - name: Run tests
-      run: |
-         docker-compose -f docker-compose-dev.yml exec  web bash -c " cd argos &&  /opt/conda/bin/python  manage.py test"
\ No newline at end of file

From 0d964ef39b1ba2d711d88a2c3bf071c3ac69b59b Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:05:33 +1100
Subject: [PATCH 07/32] Revert "move to ci file"

This reverts commit 73a9418e26c5605f218ea5dca4839c6da3130cea.
---
 .github/workflows/ci.yaml   | 21 +-----------
 .github/workflows/test.yaml | 68 +++++++++++++++++++++++++++++++++++++
 2 files changed, 69 insertions(+), 20 deletions(-)
 create mode 100644 .github/workflows/test.yaml

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 31807f6..bea8b71 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -22,15 +22,9 @@ concurrency:
 defaults:
   run:
     shell: bash -l {0}
-    
-
-jobs:
-
-  env:
-    OE_LICENSE: ${{ github.workspace }}/.OpenEye/oe_license.txt
-
 
 
+jobs:
   build:
     runs-on: ubuntu-latest
 
@@ -47,19 +41,6 @@ jobs:
       run: |
         cp devtools/deployment/.env.example .env
 
-    - name: Make .OpenEye directory
-      run: |
-        mkdir -p ${{ github.workspace }}/.OpenEye
-
-
-    - name: Test OE License & Write License to File
-      env:
-        OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
-      run: |
-        echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
-        python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'"
-
-
     - name: Build and run containers
       run: |
          docker-compose -f docker-compose-dev.yml up -d
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
new file mode 100644
index 0000000..31807f6
--- /dev/null
+++ b/.github/workflows/test.yaml
@@ -0,0 +1,68 @@
+name: ci
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    # Nightly tests run on main by default:
+    #   Scheduled workflows run on the latest commit on the default or base branch.
+    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+    - cron: "0 0 * * *"
+  workflow_dispatch:
+  merge_group:
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+    
+
+jobs:
+
+  env:
+    OE_LICENSE: ${{ github.workspace }}/.OpenEye/oe_license.txt
+
+
+
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Install docker-compose
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y docker-compose
+    
+    - name: Copy example env file
+      run: |
+        cp devtools/deployment/.env.example .env
+
+    - name: Make .OpenEye directory
+      run: |
+        mkdir -p ${{ github.workspace }}/.OpenEye
+
+
+    - name: Test OE License & Write License to File
+      env:
+        OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
+      run: |
+        echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
+        python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'"
+
+
+    - name: Build and run containers
+      run: |
+         docker-compose -f docker-compose-dev.yml up -d
+    - name: Run tests
+      run: |
+         docker-compose -f docker-compose-dev.yml exec  web bash -c " cd argos &&  /opt/conda/bin/python  manage.py test"
\ No newline at end of file

From 129f69988f0b0df0dc3acf13dff6923a72e40281 Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:07:35 +1100
Subject: [PATCH 08/32] collapse to one file

---
 .github/workflows/ci.yaml   |  4 +++
 .github/workflows/test.yaml | 68 -------------------------------------
 2 files changed, 4 insertions(+), 68 deletions(-)
 delete mode 100644 .github/workflows/test.yaml

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index bea8b71..a8b3a75 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -41,6 +41,10 @@ jobs:
       run: |
         cp devtools/deployment/.env.example .env
 
+    - name: Make OpenEye directory
+      run: |
+         mkdir -p ${{ github.workspace }}/.OpenEye
+
     - name: Build and run containers
       run: |
          docker-compose -f docker-compose-dev.yml up -d
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
deleted file mode 100644
index 31807f6..0000000
--- a/.github/workflows/test.yaml
+++ /dev/null
@@ -1,68 +0,0 @@
-name: ci
-
-on:
-  push:
-    branches:
-      - "main"
-  pull_request:
-    branches:
-      - "main"
-  schedule:
-    # Nightly tests run on main by default:
-    #   Scheduled workflows run on the latest commit on the default or base branch.
-    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
-    - cron: "0 0 * * *"
-  workflow_dispatch:
-  merge_group:
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.ref }}"
-  cancel-in-progress: true
-
-defaults:
-  run:
-    shell: bash -l {0}
-    
-
-jobs:
-
-  env:
-    OE_LICENSE: ${{ github.workspace }}/.OpenEye/oe_license.txt
-
-
-
-  build:
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Checkout code
-      uses: actions/checkout@v2
-
-    - name: Install docker-compose
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y docker-compose
-    
-    - name: Copy example env file
-      run: |
-        cp devtools/deployment/.env.example .env
-
-    - name: Make .OpenEye directory
-      run: |
-        mkdir -p ${{ github.workspace }}/.OpenEye
-
-
-    - name: Test OE License & Write License to File
-      env:
-        OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
-      run: |
-        echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
-        python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'"
-
-
-    - name: Build and run containers
-      run: |
-         docker-compose -f docker-compose-dev.yml up -d
-    - name: Run tests
-      run: |
-         docker-compose -f docker-compose-dev.yml exec  web bash -c " cd argos &&  /opt/conda/bin/python  manage.py test"
\ No newline at end of file

From d349469577ab8ee246ed7200a5fcfba335685438 Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:09:14 +1100
Subject: [PATCH 09/32] fix indents

---
 .github/workflows/ci.yaml | 47 +++++++++++++++++++--------------------
 1 file changed, 23 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index a8b3a75..a20c76b 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -13,7 +13,6 @@ on:
     #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
     - cron: "0 0 * * *"
   workflow_dispatch:
-  merge_group:
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.ref }}"
@@ -23,31 +22,31 @@ defaults:
   run:
     shell: bash -l {0}
 
-
 jobs:
   build:
     runs-on: ubuntu-latest
 
     steps:
-    - name: Checkout code
-      uses: actions/checkout@v2
-
-    - name: Install docker-compose
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y docker-compose
-    
-    - name: Copy example env file
-      run: |
-        cp devtools/deployment/.env.example .env
-
-    - name: Make OpenEye directory
-      run: |
-         mkdir -p ${{ github.workspace }}/.OpenEye
-
-    - name: Build and run containers
-      run: |
-         docker-compose -f docker-compose-dev.yml up -d
-    - name: Run tests
-      run: |
-         docker-compose -f docker-compose-dev.yml exec  web bash -c " cd argos &&  /opt/conda/bin/python  manage.py test"
\ No newline at end of file
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Install docker-compose
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y docker-compose
+      
+      - name: Copy example env file
+        run: |
+          cp devtools/deployment/.env.example .env
+
+      - name: Make OpenEye directory
+        run: |
+          mkdir -p ${{ github.workspace }}/.OpenEye
+
+      - name: Build and run containers
+        run: |
+          docker-compose -f docker-compose-dev.yml up -d
+
+      - name: Run tests
+        run: |
+          docker-compose -f docker-compose-dev.yml exec web bash -c "cd argos && /opt/conda/bin/python manage.py test"

From 2474c4310acaef62900726349068ea43e10b4226 Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:13:24 +1100
Subject: [PATCH 10/32] try some stuff

---
 .github/workflows/ci.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index a20c76b..7aec30a 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -42,6 +42,9 @@ jobs:
       - name: Make OpenEye directory
         run: |
           mkdir -p ${{ github.workspace }}/.OpenEye
+          cd ${{ github.workspace }}/.OpenEye
+          pwd
+          touch oe_license.txt
 
       - name: Build and run containers
         run: |

From 1294206d0dabd0b806e9f13422d601449c460d3f Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:14:42 +1100
Subject: [PATCH 11/32] add ci to correct path

---
 .github/workflows/ci.yaml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 7aec30a..20ecece 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -41,10 +41,8 @@ jobs:
 
       - name: Make OpenEye directory
         run: |
-          mkdir -p ${{ github.workspace }}/.OpenEye
-          cd ${{ github.workspace }}/.OpenEye
-          pwd
-          touch oe_license.txt
+          mkdir -p ~/.OpenEye
+          touch ~/.OpenEye/oe_license.txt
 
       - name: Build and run containers
         run: |

From 4507072cfcfdafaafe9759ab7beb6050604651bc Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:19:03 +1100
Subject: [PATCH 12/32] fix TTY issues

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

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 20ecece..b0f000c 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -50,4 +50,4 @@ jobs:
 
       - name: Run tests
         run: |
-          docker-compose -f docker-compose-dev.yml exec web bash -c "cd argos && /opt/conda/bin/python manage.py test"
+          docker-compose -f docker-compose-dev.yml exec -T web bash -c "cd argos && /opt/conda/bin/python manage.py test"

From 298cb1081dde64d2108ce0e4e9fccfa6ed26655c Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:33:04 +1100
Subject: [PATCH 13/32] try waiting

---
 .github/workflows/ci.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index b0f000c..98b29ef 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -47,6 +47,12 @@ jobs:
       - name: Build and run containers
         run: |
           docker-compose -f docker-compose-dev.yml up -d
+          docker container ls
+
+      - name: wait for containers to start
+        run: |
+          sleep 30
+          docker container ls
 
       - name: Run tests
         run: |

From 5f77ff35623356896202fd368e0a4ebfc9e56577 Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:42:20 +1100
Subject: [PATCH 14/32] try with healthcheck instead

---
 .github/workflows/ci.yaml | 8 ++++----
 docker-compose-dev.yml    | 7 +++++++
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 98b29ef..9404d5c 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -49,10 +49,10 @@ jobs:
           docker-compose -f docker-compose-dev.yml up -d
           docker container ls
 
-      - name: wait for containers to start
-        run: |
-          sleep 30
-          docker container ls
+      # - name: wait for containers to start
+      #   run: |
+      #     sleep 30
+      #     docker container ls
 
       - name: Run tests
         run: |
diff --git a/docker-compose-dev.yml b/docker-compose-dev.yml
index 3926887..aa2fbc9 100644
--- a/docker-compose-dev.yml
+++ b/docker-compose-dev.yml
@@ -23,6 +23,13 @@ services:
 
   db:
     image: postgres:15-alpine
+    
+    healthcheck:
+      test: pg_isready
+      interval: 5s
+      timeout: 10s
+      retries: 120
+    
     volumes:
       - postgres_data:/var/lib/postgresql/data/
     expose:

From 1632b523ad22b5cf7a7bbe506e42698da77b146f Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:48:27 +1100
Subject: [PATCH 15/32] try making sure service is healthy

---
 docker-compose-dev.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docker-compose-dev.yml b/docker-compose-dev.yml
index aa2fbc9..1c67350 100644
--- a/docker-compose-dev.yml
+++ b/docker-compose-dev.yml
@@ -16,7 +16,9 @@ services:
     env_file:
       - .env
     depends_on:
-      - db
+      db:
+        condition: service_healthy
+
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.django.rule=Host(`django.localhost`)"

From 472a5f7adbc3312253b6c4d601186c386a509a2f Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Thu, 8 Feb 2024 17:57:13 +1100
Subject: [PATCH 16/32] add initial testing

---
 .github/workflows/ci.yaml   |  5 -----
 argos/argos_viewer/tests.py |  2 --
 docker-compose-prod.yml     | 10 +++++++++-
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 9404d5c..be38497 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -49,11 +49,6 @@ jobs:
           docker-compose -f docker-compose-dev.yml up -d
           docker container ls
 
-      # - name: wait for containers to start
-      #   run: |
-      #     sleep 30
-      #     docker container ls
-
       - name: Run tests
         run: |
           docker-compose -f docker-compose-dev.yml exec -T web bash -c "cd argos && /opt/conda/bin/python manage.py test"
diff --git a/argos/argos_viewer/tests.py b/argos/argos_viewer/tests.py
index be7ee9d..14c0393 100644
--- a/argos/argos_viewer/tests.py
+++ b/argos/argos_viewer/tests.py
@@ -6,5 +6,3 @@ class BlankTest(TestCase):
     def test_placeholder(self):
         self.assertEqual(1, 1)
 
-    def test_fail(self):
-        self.assertEqual(1,2)
diff --git a/docker-compose-prod.yml b/docker-compose-prod.yml
index 9151d41..46e3afe 100644
--- a/docker-compose-prod.yml
+++ b/docker-compose-prod.yml
@@ -17,7 +17,8 @@ services:
     env_file:
       - .env
     depends_on:
-      - db
+      db:
+        condition: service_healthy
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.django.rule=Host(`${HOST_DOMAIN:?err}`)"
@@ -27,6 +28,13 @@ services:
 
   db:
     image: postgres:15-alpine
+
+    healthcheck:
+      test: pg_isready
+      interval: 5s
+      timeout: 10s
+      retries: 120
+
     volumes:
       - postgres_data_prod:/var/lib/postgresql/data/
     expose:

From 28c2958877cde616d9a59252ab172d8f61c50116 Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Fri, 9 Feb 2024 13:58:54 +1100
Subject: [PATCH 17/32] add updates

---
 argos/argos/settings.py                     |  1 +
 argos/argos_viewer/models.py                |  2 ++
 argos/argos_viewer/tests.py                 | 39 ++++++++++++++++++---
 devtools/conda-envs/argos-ubuntu-latest.yml |  4 ++-
 4 files changed, 41 insertions(+), 5 deletions(-)

diff --git a/argos/argos/settings.py b/argos/argos/settings.py
index fd7e91a..32b3b87 100644
--- a/argos/argos/settings.py
+++ b/argos/argos/settings.py
@@ -48,6 +48,7 @@
     'django.contrib.sessions',
     'django.contrib.messages',
     'django.contrib.staticfiles',
+    'django_cleanup.apps.CleanupConfig',
     'argos_viewer.apps.ArgosViewerConfig',
 
 ]
diff --git a/argos/argos_viewer/models.py b/argos/argos_viewer/models.py
index 8b094f8..742d528 100644
--- a/argos/argos_viewer/models.py
+++ b/argos/argos_viewer/models.py
@@ -10,3 +10,5 @@ class TargetPDBFile(models.Model):
     pdb_file = models.ForeignKey(PDBFile, on_delete=models.CASCADE)
     target = models.CharField(max_length=200)
     upload_date = models.DateTimeField(auto_now_add=True)
+
+
diff --git a/argos/argos_viewer/tests.py b/argos/argos_viewer/tests.py
index 14c0393..a569419 100644
--- a/argos/argos_viewer/tests.py
+++ b/argos/argos_viewer/tests.py
@@ -1,8 +1,39 @@
 from django.test import TestCase
+from .models import PDBFile, TargetPDBFile
+from django.core.files.uploadedfile import SimpleUploadedFile
+from django.utils import timezone
+import os
 
-# Create your tests here.
+class PDBFileModelTest(TestCase):
+    def setUp(self):
+        self.file = SimpleUploadedFile("test.pdb", b"pdb file content")
+        self.pdb_file = PDBFile.objects.create(file=self.file)
 
-class BlankTest(TestCase):
-    def test_placeholder(self):
-        self.assertEqual(1, 1)
 
+    def test_pdb_file_created(self):
+        self.assertTrue(os.path.exists(self.pdb_file.file.path))
+
+    def test_file_extension(self):
+        self.assertEqual(self.pdb_file.file.name.split(".")[-1], "pdb")
+
+class TargetPDBFileModelTest(TestCase):
+    def setUp(self):
+        self.file = SimpleUploadedFile("test.pdb", b"pdb file content")
+        self.pdb_file = PDBFile.objects.create(file=self.file)
+        self.target_pdb_file = TargetPDBFile.objects.create(pdb_file=self.pdb_file, target="test_target", upload_date=timezone.now())
+
+    def tearDown(self):
+        os.remove(self.file.name)
+
+    def test_target_pdb_file_created(self):
+        self.assertTrue(TargetPDBFile.objects.exists())
+
+    def test_target(self):
+        self.assertEqual(self.target_pdb_file.target, "test_target")
+
+    def test_upload_date(self):
+        self.assertIsNotNone(self.target_pdb_file.upload_date)
+
+    def test_pdb_file_deletion_on_target_pdb_file_deletion(self):
+        self.target_pdb_file.delete()
+        self.assertFalse(os.path.exists(self.pdb_file.file.path))
diff --git a/devtools/conda-envs/argos-ubuntu-latest.yml b/devtools/conda-envs/argos-ubuntu-latest.yml
index 7e3387d..862d2d1 100644
--- a/devtools/conda-envs/argos-ubuntu-latest.yml
+++ b/devtools/conda-envs/argos-ubuntu-latest.yml
@@ -12,11 +12,13 @@ dependencies:
   # argos deps
   - django
   - gunicorn
+  - django-cleanup
+
 
   # Testing
   - pytest
   - pytest-cov
-
+  - pooch
 
   # asapdiscovery deps
 

From d5a16fbe4e960e0f6a59e95a61937169da9d12cd Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Fri, 9 Feb 2024 14:11:00 +1100
Subject: [PATCH 18/32] make model tests work

---
 argos/argos_viewer/models.py | 14 +++++++++++++-
 argos/argos_viewer/tests.py  |  3 ++-
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/argos/argos_viewer/models.py b/argos/argos_viewer/models.py
index 742d528..9a8966c 100644
--- a/argos/argos_viewer/models.py
+++ b/argos/argos_viewer/models.py
@@ -1,10 +1,17 @@
+from typing import Any
 from django.db import models
 from django.core.validators import FileExtensionValidator
-
+import os
 
 class PDBFile(models.Model):
     file = models.FileField(validators=[FileExtensionValidator(['pdb'])], upload_to="pdb_data")
 
+    def delete(self, *args, **kwargs):
+        # Delete the file when the instance is deleted
+        if self.file:
+            if os.path.isfile(self.file.path):
+                os.remove(self.file.path)
+        super(PDBFile, self).delete(*args, **kwargs)
 
 class TargetPDBFile(models.Model):
     pdb_file = models.ForeignKey(PDBFile, on_delete=models.CASCADE)
@@ -12,3 +19,8 @@ class TargetPDBFile(models.Model):
     upload_date = models.DateTimeField(auto_now_add=True)
 
 
+    def delete(self, *args, **kwargs):
+        # Delete the associated PDBFile instance, which should trigger its delete method
+        if self.pdb_file:
+            self.pdb_file.delete()
+        super(TargetPDBFile, self).delete(*args, **kwargs)
\ No newline at end of file
diff --git a/argos/argos_viewer/tests.py b/argos/argos_viewer/tests.py
index a569419..abbc4cf 100644
--- a/argos/argos_viewer/tests.py
+++ b/argos/argos_viewer/tests.py
@@ -23,7 +23,8 @@ def setUp(self):
         self.target_pdb_file = TargetPDBFile.objects.create(pdb_file=self.pdb_file, target="test_target", upload_date=timezone.now())
 
     def tearDown(self):
-        os.remove(self.file.name)
+        if os.path.exists(self.target_pdb_file.pdb_file.file.path):
+            os.remove(self.target_pdb_file.pdb_file.file.path)
 
     def test_target_pdb_file_created(self):
         self.assertTrue(TargetPDBFile.objects.exists())

From ed5f687643c2d9d85e4123956188a71974c344b8 Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Fri, 9 Feb 2024 14:19:43 +1100
Subject: [PATCH 19/32] make tests even better

---
 argos/argos_viewer/tests/__init__.py          |  0
 .../{tests.py => tests/test_models.py}        |  5 +-
 argos/argos_viewer/tests/test_urls.py         | 28 +++++++++++
 argos/argos_viewer/tests/test_views.py        | 49 +++++++++++++++++++
 4 files changed, 81 insertions(+), 1 deletion(-)
 create mode 100644 argos/argos_viewer/tests/__init__.py
 rename argos/argos_viewer/{tests.py => tests/test_models.py} (96%)
 create mode 100644 argos/argos_viewer/tests/test_urls.py
 create mode 100644 argos/argos_viewer/tests/test_views.py

diff --git a/argos/argos_viewer/tests/__init__.py b/argos/argos_viewer/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/argos/argos_viewer/tests.py b/argos/argos_viewer/tests/test_models.py
similarity index 96%
rename from argos/argos_viewer/tests.py
rename to argos/argos_viewer/tests/test_models.py
index abbc4cf..b914619 100644
--- a/argos/argos_viewer/tests.py
+++ b/argos/argos_viewer/tests/test_models.py
@@ -1,5 +1,5 @@
 from django.test import TestCase
-from .models import PDBFile, TargetPDBFile
+from argos_viewer.models import PDBFile, TargetPDBFile
 from django.core.files.uploadedfile import SimpleUploadedFile
 from django.utils import timezone
 import os
@@ -38,3 +38,6 @@ def test_upload_date(self):
     def test_pdb_file_deletion_on_target_pdb_file_deletion(self):
         self.target_pdb_file.delete()
         self.assertFalse(os.path.exists(self.pdb_file.file.path))
+
+
+
diff --git a/argos/argos_viewer/tests/test_urls.py b/argos/argos_viewer/tests/test_urls.py
new file mode 100644
index 0000000..52f6e2c
--- /dev/null
+++ b/argos/argos_viewer/tests/test_urls.py
@@ -0,0 +1,28 @@
+from django.test import SimpleTestCase
+from django.urls import reverse, resolve
+from argos_viewer.views import home, upload_sucessful, TargetPDBListView, target_pdb_detail_view, failed, no_fitness_data
+
+class TestUrls(SimpleTestCase):
+    def test_home_url_resolves(self):
+        url = reverse('home')
+        self.assertEqual(resolve(url).func, home)
+
+    def test_upload_sucessful_url_resolves(self):
+        url = reverse('upload_sucessful')
+        self.assertEqual(resolve(url).func, upload_sucessful)
+
+    def test_pdb_files_url_resolves(self):
+        url = reverse('pdb_files')
+        self.assertEqual(resolve(url).func.view_class, TargetPDBListView)
+
+    def test_detail_url_resolves(self):
+        url = reverse('detail', args=[1])  # assuming pk=1
+        self.assertEqual(resolve(url).func, target_pdb_detail_view)
+
+    def test_failed_url_resolves(self):
+        url = reverse('failed')
+        self.assertEqual(resolve(url).func, failed)
+
+    def test_no_fitness_data_url_resolves(self):
+        url = reverse('no_fitness_data', args=['target_name'])
+        self.assertEqual(resolve(url).func, no_fitness_data)
diff --git a/argos/argos_viewer/tests/test_views.py b/argos/argos_viewer/tests/test_views.py
new file mode 100644
index 0000000..101eb26
--- /dev/null
+++ b/argos/argos_viewer/tests/test_views.py
@@ -0,0 +1,49 @@
+from django.test import TestCase, Client
+from django.urls import reverse
+from argos_viewer.models import PDBFile, TargetPDBFile
+from django.contrib.auth.models import User
+
+
+class ViewTests(TestCase):
+    def setUp(self):
+        # Create a user
+        self.user = User.objects.create_user(username='testuser', password='12345')
+
+    def test_index_view(self):
+        response = self.client.get(reverse('index'))
+        self.assertEqual(response.status_code, 302)  # Redirects to home
+
+    def test_home_view_GET(self):
+        self.client.force_login(self.user)
+        response = self.client.get(reverse('home'))
+        self.assertEqual(response.status_code, 200)
+        self.assertTemplateUsed(response, 'argos_viewer/home.html')
+
+    def test_upload_successful_view(self):
+        self.client.force_login(self.user)
+        response = self.client.get(reverse('upload_sucessful'))
+        self.assertEqual(response.status_code, 200)
+        self.assertContains(response, 'upload worked!')
+
+    # You can write similar tests for other views...
+
+    def test_target_pdb_detail_view_GET(self):
+        self.client.force_login(self.user)
+        target_pdb = TargetPDBFile.objects.create()
+        response = self.client.get(reverse('detail', args=[target_pdb.pk]))
+        self.assertEqual(response.status_code, 200)
+        # Make assertions based on the response content or template used
+
+    def test_failed_view_GET(self):
+        self.client.force_login(self.user)
+        response = self.client.get(reverse('failed'))
+        self.assertEqual(response.status_code, 200)
+        self.assertTemplateUsed(response, 'argos_viewer/failed.html')
+
+    def test_no_fitness_data_view_GET(self):
+        self.client.force_login(self.user)
+        response = self.client.get(reverse('no_fitness_data', args=['target_name']))
+        self.assertEqual(response.status_code, 200)
+        self.assertTemplateUsed(response, 'argos_viewer/no_fitness_data.html')
+
+    # Add tests for POST requests as well if necessary

From d40eb8c7f3edc6f10265a8cf0a4b29e3fa59c966 Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Fri, 9 Feb 2024 14:25:58 +1100
Subject: [PATCH 20/32] improve again

---
 argos/argos_viewer/tests/test_views.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/argos/argos_viewer/tests/test_views.py b/argos/argos_viewer/tests/test_views.py
index 101eb26..ff33481 100644
--- a/argos/argos_viewer/tests/test_views.py
+++ b/argos/argos_viewer/tests/test_views.py
@@ -1,6 +1,8 @@
 from django.test import TestCase, Client
 from django.urls import reverse
 from argos_viewer.models import PDBFile, TargetPDBFile
+from django.core.files.uploadedfile import SimpleUploadedFile
+from django.utils import timezone
 from django.contrib.auth.models import User
 
 
@@ -8,6 +10,9 @@ class ViewTests(TestCase):
     def setUp(self):
         # Create a user
         self.user = User.objects.create_user(username='testuser', password='12345')
+        self.file = SimpleUploadedFile("test.pdb", b"pdb file content")
+        self.pdb_file = PDBFile.objects.create(file=self.file)
+        self.target_pdb_file = TargetPDBFile.objects.create(pdb_file=self.pdb_file, target="test_target", upload_date=timezone.now())
 
     def test_index_view(self):
         response = self.client.get(reverse('index'))
@@ -25,14 +30,12 @@ def test_upload_successful_view(self):
         self.assertEqual(response.status_code, 200)
         self.assertContains(response, 'upload worked!')
 
-    # You can write similar tests for other views...
 
     def test_target_pdb_detail_view_GET(self):
         self.client.force_login(self.user)
-        target_pdb = TargetPDBFile.objects.create()
-        response = self.client.get(reverse('detail', args=[target_pdb.pk]))
+        response = self.client.get(reverse('detail', args=[self.target_pdb_file.pk]))
         self.assertEqual(response.status_code, 200)
-        # Make assertions based on the response content or template used
+        self.assertTemplateUsed(response, 'argos_viewer/detail.html')
 
     def test_failed_view_GET(self):
         self.client.force_login(self.user)

From 74bf28a702df015738c4a95ab2686c38c4395a21 Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Fri, 9 Feb 2024 15:56:26 +1100
Subject: [PATCH 21/32] get tests partially working

---
 argos/argos/settings.py                           | 15 +++++++++++++++
 .../argos_viewer/target_pdb_detail_view.html      |  1 -
 argos/argos_viewer/tests/test_views.py            | 11 +++++++----
 argos/argos_viewer/views.py                       | 13 ++++++++-----
 4 files changed, 30 insertions(+), 10 deletions(-)
 delete mode 100644 argos/argos_viewer/templates/argos_viewer/target_pdb_detail_view.html

diff --git a/argos/argos/settings.py b/argos/argos/settings.py
index 32b3b87..7241fd3 100644
--- a/argos/argos/settings.py
+++ b/argos/argos/settings.py
@@ -147,3 +147,18 @@
 
 # Redirect to home URL after login (Default redirects to /accounts/profile/)
 LOGIN_REDIRECT_URL = '/'
+
+
+LOGGING = {
+    "version": 1,
+    "disable_existing_loggers": False,
+    "handlers": {
+        "console": {"class": "logging.StreamHandler"},
+    },
+    "loggers": {
+        "django": {
+            "handlers": ["console"],
+            "level": "INFO",
+        },
+    }
+}
diff --git a/argos/argos_viewer/templates/argos_viewer/target_pdb_detail_view.html b/argos/argos_viewer/templates/argos_viewer/target_pdb_detail_view.html
deleted file mode 100644
index f3ca97f..0000000
--- a/argos/argos_viewer/templates/argos_viewer/target_pdb_detail_view.html
+++ /dev/null
@@ -1 +0,0 @@
-{{html_content}}
\ No newline at end of file
diff --git a/argos/argos_viewer/tests/test_views.py b/argos/argos_viewer/tests/test_views.py
index ff33481..3b24268 100644
--- a/argos/argos_viewer/tests/test_views.py
+++ b/argos/argos_viewer/tests/test_views.py
@@ -1,6 +1,7 @@
-from django.test import TestCase, Client
+from django.test import TestCase, Client, RequestFactory
 from django.urls import reverse
 from argos_viewer.models import PDBFile, TargetPDBFile
+from argos_viewer.views import target_pdb_detail_view
 from django.core.files.uploadedfile import SimpleUploadedFile
 from django.utils import timezone
 from django.contrib.auth.models import User
@@ -12,7 +13,7 @@ def setUp(self):
         self.user = User.objects.create_user(username='testuser', password='12345')
         self.file = SimpleUploadedFile("test.pdb", b"pdb file content")
         self.pdb_file = PDBFile.objects.create(file=self.file)
-        self.target_pdb_file = TargetPDBFile.objects.create(pdb_file=self.pdb_file, target="test_target", upload_date=timezone.now())
+        self.target_pdb_file = TargetPDBFile.objects.create(pdb_file=self.pdb_file, target="SARS-CoV-2-Mpro", upload_date=timezone.now())
 
     def test_index_view(self):
         response = self.client.get(reverse('index'))
@@ -33,9 +34,11 @@ def test_upload_successful_view(self):
 
     def test_target_pdb_detail_view_GET(self):
         self.client.force_login(self.user)
-        response = self.client.get(reverse('detail', args=[self.target_pdb_file.pk]))
+        print("HELLO")
+        response = self.client.get(reverse('detail', args=[self.target_pdb_file.pk]), follow=True)
+        print(response)
+        print(response.content)
         self.assertEqual(response.status_code, 200)
-        self.assertTemplateUsed(response, 'argos_viewer/detail.html')
 
     def test_failed_view_GET(self):
         self.client.force_login(self.user)
diff --git a/argos/argos_viewer/views.py b/argos/argos_viewer/views.py
index e1d67ba..60454c3 100644
--- a/argos/argos_viewer/views.py
+++ b/argos/argos_viewer/views.py
@@ -15,6 +15,10 @@
 from asapdiscovery.data.fitness import target_has_fitness_data
 import tempfile
 
+import logging
+
+logger = logging.getLogger('django')
+
 def index(request):
     context = {}
     return redirect("home")
@@ -74,14 +78,13 @@ def target_pdb_detail_view(request, pk):
             target_kwargs={"target_name": "unknown"},
         )
 
-        tf = tempfile.NamedTemporaryFile()  
+        tf = tempfile.NamedTemporaryFile()
         html_viz = HTMLVisualizer(
-            [c.ligand.to_oemol()], [tf], obj.target, c.target.to_oemol(), color_method="fitness", align=False 
-        )
-        # align=True is broken, see https://github.com/choderalab/asapdiscovery/issues/709
+            [c.ligand.to_oemol()], [tf], obj.target, c.target.to_oemol(), color_method="fitness", align=True)
         html = html_viz.make_poses_html()[0]
+        logger.debug("Made pose html")
     except Exception as e:
-        print(f"rendering failed with exception {e}")
+        logger.error(f"rendering failed with exception {e}")
         return redirect("failed")
 
     return HttpResponse(html)

From 0af693b813a3d998c7088d5276bb999c102ca51c Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Fri, 9 Feb 2024 16:29:40 +1100
Subject: [PATCH 22/32] try

---
 argos/argos/settings.py                     | 3 ++-
 argos/argos_viewer/tests/test_oe_license.py | 6 ++++++
 argos/argos_viewer/tests/test_views.py      | 1 -
 3 files changed, 8 insertions(+), 2 deletions(-)
 create mode 100644 argos/argos_viewer/tests/test_oe_license.py

diff --git a/argos/argos/settings.py b/argos/argos/settings.py
index 7241fd3..913958d 100644
--- a/argos/argos/settings.py
+++ b/argos/argos/settings.py
@@ -89,7 +89,8 @@
 # https://docs.djangoproject.com/en/4.2/ref/settings/#databases
 
 DATABASES = {
-    'default': env.db(),
+    'default': env.db().update({"TEST": {"NAME": "test_db"}}),
+
 }
 
 
diff --git a/argos/argos_viewer/tests/test_oe_license.py b/argos/argos_viewer/tests/test_oe_license.py
new file mode 100644
index 0000000..17662ee
--- /dev/null
+++ b/argos/argos_viewer/tests/test_oe_license.py
@@ -0,0 +1,6 @@
+from django.test import TestCase
+
+class OELicenseTests(TestCase):
+    def test_oechem_is_licensed(self):
+        from asapdiscovery.data.openeye import oechem
+        self.assertTrue(oechem.OEChemIsLicensed())
\ No newline at end of file
diff --git a/argos/argos_viewer/tests/test_views.py b/argos/argos_viewer/tests/test_views.py
index 3b24268..06d12cf 100644
--- a/argos/argos_viewer/tests/test_views.py
+++ b/argos/argos_viewer/tests/test_views.py
@@ -1,7 +1,6 @@
 from django.test import TestCase, Client, RequestFactory
 from django.urls import reverse
 from argos_viewer.models import PDBFile, TargetPDBFile
-from argos_viewer.views import target_pdb_detail_view
 from django.core.files.uploadedfile import SimpleUploadedFile
 from django.utils import timezone
 from django.contrib.auth.models import User

From 81f60b68d8765bfbf77c2c413ed566c2ebe769ac Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Fri, 9 Feb 2024 16:33:27 +1100
Subject: [PATCH 23/32] inject OE license

---
 .github/workflows/ci.yaml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index be38497..3e136db 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -42,7 +42,12 @@ jobs:
       - name: Make OpenEye directory
         run: |
           mkdir -p ~/.OpenEye
-          touch ~/.OpenEye/oe_license.txt
+      
+      - name: Copy OpenEye license file
+        env:
+          OE_LICENSE: ${{ secrets.OE_LICENSE }}
+        run: |
+          echo "$OE_LICENSE" > ~/.OpenEye/oe_license.txt
 
       - name: Build and run containers
         run: |

From 29d9ee2f9cbe801e3cd1daa2653fdf45950b1b0a Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Fri, 9 Feb 2024 16:46:19 +1100
Subject: [PATCH 24/32] fix settings stuff

---
 argos/argos/settings.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/argos/argos/settings.py b/argos/argos/settings.py
index 913958d..6f95457 100644
--- a/argos/argos/settings.py
+++ b/argos/argos/settings.py
@@ -89,7 +89,7 @@
 # https://docs.djangoproject.com/en/4.2/ref/settings/#databases
 
 DATABASES = {
-    'default': env.db().update({"TEST": {"NAME": "test_db"}}),
+    'default': env.db(),
 
 }
 

From b91d3a28b860d6fc778d7b19bf02911828cea55a Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Sat, 10 Feb 2024 00:24:29 +1100
Subject: [PATCH 25/32] HOLY GUACAMOLE it was the OE version

---
 Dockerfile                                  | 17 +++++++++++++++--
 devtools/conda-envs/argos-ubuntu-latest.yml |  2 +-
 docker-compose-dev.yml                      |  8 ++++----
 docker-compose-prod.yml                     |  2 +-
 4 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 2737df3..ca28ae2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,17 @@
 # Use the conda-forge base image with Python
 FROM mambaorg/micromamba:jammy
 
+
+ARG USER_ID
+ARG GROUP_ID
+
+USER root
+
+RUN addgroup --gid $GROUP_ID user
+RUN adduser --disabled-password --gecos '' --uid $USER_ID --gid $GROUP_ID user
+USER user
+
+
 # set environment variables
 ENV PYTHONUNBUFFERED 1
 
@@ -13,15 +24,17 @@ COPY . /argos
 RUN micromamba config append channels conda-forge 
 RUN  micromamba config append channels openeye
 
-COPY --chown=$MAMBA_USER:$MAMBA_USER devtools/conda-envs/argos-ubuntu-latest.yml /tmp/env.yaml
+COPY --chown=user:user devtools/conda-envs/argos-ubuntu-latest.yml /tmp/env.yaml
 
 RUN micromamba install -y -n base git -f /tmp/env.yaml && \
     micromamba clean --all --yes
 
 USER root
 RUN mkdir /openeye
+RUN chown -R user:user /openeye
 RUN mkdir /argos/pdb_data
-USER $MAMBA_USER
+RUN chown -R user:user /argos/pdb_data
+USER user
 ENV OE_LICENSE=/openeye/oe_license.txt
 
 
diff --git a/devtools/conda-envs/argos-ubuntu-latest.yml b/devtools/conda-envs/argos-ubuntu-latest.yml
index 862d2d1..6e627ad 100644
--- a/devtools/conda-envs/argos-ubuntu-latest.yml
+++ b/devtools/conda-envs/argos-ubuntu-latest.yml
@@ -24,7 +24,7 @@ dependencies:
 
   # Others
   - appdirs
-  - openeye-toolkits
+  - openeye-toolkits <2023.2.3
   - pydantic >=1.10.8,<2.0.0a0
 
   # data
diff --git a/docker-compose-dev.yml b/docker-compose-dev.yml
index 1c67350..0e1f80d 100644
--- a/docker-compose-dev.yml
+++ b/docker-compose-dev.yml
@@ -27,7 +27,7 @@ services:
     image: postgres:15-alpine
     
     healthcheck:
-      test: pg_isready
+      test: pg_isready -U ${POSTGRES_USER:?err} -d ${POSTGRES_DB:?err}
       interval: 5s
       timeout: 10s
       retries: 120
@@ -37,9 +37,9 @@ services:
     expose:
       - 5432
     environment:
-      - POSTGRES_USER=django_traefik
-      - POSTGRES_PASSWORD=django_traefik
-      - POSTGRES_DB=django_traefik
+      - POSTGRES_USER=${POSTGRES_USER:?err}
+      - POSTGRES_PASSWORD=${POSTGRES_PASSWORD:?err}
+      - POSTGRES_DB=${POSTGRES_DB:?err}
 
   traefik: 
     image: traefik:latest
diff --git a/docker-compose-prod.yml b/docker-compose-prod.yml
index 46e3afe..0c0a751 100644
--- a/docker-compose-prod.yml
+++ b/docker-compose-prod.yml
@@ -30,7 +30,7 @@ services:
     image: postgres:15-alpine
 
     healthcheck:
-      test: pg_isready
+      test: pg_isready -U ${POSTGRES_USER:?err} -d ${POSTGRES_DB:?err}
       interval: 5s
       timeout: 10s
       retries: 120

From 8e543615ff4d653f7d5ac55446f908959b437d41 Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Sat, 10 Feb 2024 00:29:05 +1100
Subject: [PATCH 26/32] fix wf

---
 .github/workflows/ci.yaml | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 3e136db..5d81c71 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -49,11 +49,16 @@ jobs:
         run: |
           echo "$OE_LICENSE" > ~/.OpenEye/oe_license.txt
 
-      - name: Build and run containers
+      - name: Build containers
         run: |
-          docker-compose -f docker-compose-dev.yml up -d
+          docker-compose -f docker-compose-dev.yml  build  --build-arg USER_ID=$(id -u) --build-arg GROUP_ID=$(id -g)        
           docker container ls
+          docker-compose -f docker-compose-dev.yml  up -d
+
+      - name: Chown volume
+        run: |
+          chown -R $(id -u):$(id -g) argos/pdb_data
 
       - name: Run tests
         run: |
-          docker-compose -f docker-compose-dev.yml exec -T web bash -c "cd argos && /opt/conda/bin/python manage.py test"
+          docker-compose -f docker-compose-dev.yml exec -T web bash -c "cd argos && /opt/conda/bin/python manage.py test --no-input"

From ca40809138e98c7d23718b0677a8d4ffd296b1ac Mon Sep 17 00:00:00 2001
From: hmacdope <hugomacdermott@gmail.com>
Date: Sat, 10 Feb 2024 00:33:05 +1100
Subject: [PATCH 27/32] gix path?

---
 .github/workflows/ci.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 5d81c71..3f7dd46 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -57,7 +57,9 @@ jobs:
 
       - name: Chown volume
         run: |
-          chown -R $(id -u):$(id -g) argos/pdb_data
+          ls -alsh
+          ls -alsh argos
+          chown -R $(id -u):$(id -g) argos/argos/pdb_data
 
       - name: Run tests
         run: |

From 9ead9ab6300481d6ea38e2b8e567b7791dc1cd38 Mon Sep 17 00:00:00 2001
From: Hugo MacDermott-Opeskin <hugomacdermott@gmail.com>
Date: Sun, 11 Feb 2024 18:59:03 +1100
Subject: [PATCH 28/32] Update ci.yaml

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

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 3f7dd46..9cb0fe9 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -59,7 +59,7 @@ jobs:
         run: |
           ls -alsh
           ls -alsh argos
-          chown -R $(id -u):$(id -g) argos/argos/pdb_data
+          sudo chown -R $(id -u):$(id -g) argos/argos/pdb_data
 
       - name: Run tests
         run: |

From dd9b7cb1a3859c50ef82f0363d90306d53f82302 Mon Sep 17 00:00:00 2001
From: Hugo MacDermott-Opeskin <hugomacdermott@gmail.com>
Date: Sun, 11 Feb 2024 19:02:34 +1100
Subject: [PATCH 29/32] Update ci.yaml

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

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 9cb0fe9..aacea74 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -59,7 +59,7 @@ jobs:
         run: |
           ls -alsh
           ls -alsh argos
-          sudo chown -R $(id -u):$(id -g) argos/argos/pdb_data
+          sudo chown -R $(id -u):$(id -g) argos/pdb_data
 
       - name: Run tests
         run: |

From 588237646d6d01522b37e5df83d09e8ed5146041 Mon Sep 17 00:00:00 2001
From: Hugo MacDermott-Opeskin <hugomacdermott@gmail.com>
Date: Sun, 11 Feb 2024 19:15:39 +1100
Subject: [PATCH 30/32] Update test_views.py

---
 argos/argos_viewer/tests/test_views.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/argos/argos_viewer/tests/test_views.py b/argos/argos_viewer/tests/test_views.py
index 06d12cf..a639da5 100644
--- a/argos/argos_viewer/tests/test_views.py
+++ b/argos/argos_viewer/tests/test_views.py
@@ -4,13 +4,17 @@
 from django.core.files.uploadedfile import SimpleUploadedFile
 from django.utils import timezone
 from django.contrib.auth.models import User
+from asapdiscovery.data.testing.test_resources import fetch_test_file
 
 
 class ViewTests(TestCase):
     def setUp(self):
+        self._test_file = fetch_test_file("Mpro-P2660_0A_bound.pdb")
+        with open(self._test_file, "r") as f:
+            self._file_contents = f.read()
         # Create a user
         self.user = User.objects.create_user(username='testuser', password='12345')
-        self.file = SimpleUploadedFile("test.pdb", b"pdb file content")
+        self.file = SimpleUploadedFile("test.pdb", self._file_contents)
         self.pdb_file = PDBFile.objects.create(file=self.file)
         self.target_pdb_file = TargetPDBFile.objects.create(pdb_file=self.pdb_file, target="SARS-CoV-2-Mpro", upload_date=timezone.now())
 
@@ -33,7 +37,7 @@ def test_upload_successful_view(self):
 
     def test_target_pdb_detail_view_GET(self):
         self.client.force_login(self.user)
-        print("HELLO")
+        print(self._file_contents)
         response = self.client.get(reverse('detail', args=[self.target_pdb_file.pk]), follow=True)
         print(response)
         print(response.content)

From b50f232e853c8655466e8b044c6b271734bb999b Mon Sep 17 00:00:00 2001
From: Hugo MacDermott-Opeskin <hugomacdermott@gmail.com>
Date: Sun, 11 Feb 2024 19:20:14 +1100
Subject: [PATCH 31/32] Update test_views.py

---
 argos/argos_viewer/tests/test_views.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/argos/argos_viewer/tests/test_views.py b/argos/argos_viewer/tests/test_views.py
index a639da5..61a1120 100644
--- a/argos/argos_viewer/tests/test_views.py
+++ b/argos/argos_viewer/tests/test_views.py
@@ -14,7 +14,7 @@ def setUp(self):
             self._file_contents = f.read()
         # Create a user
         self.user = User.objects.create_user(username='testuser', password='12345')
-        self.file = SimpleUploadedFile("test.pdb", self._file_contents)
+        self.file = SimpleUploadedFile("test.pdb", self._file_contents.encode())
         self.pdb_file = PDBFile.objects.create(file=self.file)
         self.target_pdb_file = TargetPDBFile.objects.create(pdb_file=self.pdb_file, target="SARS-CoV-2-Mpro", upload_date=timezone.now())
 

From 40411e42772be31441c9846c82be7cc291116ed5 Mon Sep 17 00:00:00 2001
From: Hugo MacDermott-Opeskin <hugomacdermott@gmail.com>
Date: Sun, 11 Feb 2024 19:24:33 +1100
Subject: [PATCH 32/32] Update test_views.py

---
 argos/argos_viewer/tests/test_views.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/argos/argos_viewer/tests/test_views.py b/argos/argos_viewer/tests/test_views.py
index 61a1120..e103e96 100644
--- a/argos/argos_viewer/tests/test_views.py
+++ b/argos/argos_viewer/tests/test_views.py
@@ -37,10 +37,7 @@ def test_upload_successful_view(self):
 
     def test_target_pdb_detail_view_GET(self):
         self.client.force_login(self.user)
-        print(self._file_contents)
         response = self.client.get(reverse('detail', args=[self.target_pdb_file.pk]), follow=True)
-        print(response)
-        print(response.content)
         self.assertEqual(response.status_code, 200)
 
     def test_failed_view_GET(self):