From 633176ebf629d152875098b8f03cf7f4530af73e Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Mon, 7 Oct 2024 17:42:02 +0200
Subject: [PATCH 01/49] feat: add ci pipeline [experimental]

---
 .github/workflows/pylint.yml | 18 ++++++++++++++++++
 resources/retinal-rl.def     |  3 +++
 2 files changed, 21 insertions(+)
 create mode 100644 .github/workflows/pylint.yml

diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
new file mode 100644
index 0000000..c4e9c21
--- /dev/null
+++ b/.github/workflows/pylint.yml
@@ -0,0 +1,18 @@
+name: Pylint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: eWaterCycle/setup-apptainer@v2
+      with:
+        apptainer-version: 1.3.0
+
+    - name: Build Singularity container
+      run: apptainer build retinal-rl.sif resources/retinal-rl.def
+
+    - name: Run Pylint
+      run: singularity exec retinal-rl.sif pylint $(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')
diff --git a/resources/retinal-rl.def b/resources/retinal-rl.def
index 6aef984..71ca034 100644
--- a/resources/retinal-rl.def
+++ b/resources/retinal-rl.def
@@ -59,3 +59,6 @@ From: nvidia/cuda:11.7.1-runtime-ubuntu22.04
   # retinal-rl Extra
 
   pip3 install gymnasium==0.28.1 torch==1.13.1 vizdoom==1.2.0 torchvision==0.14.1 matplotlib opentsne pygame pycairo git+https://github.com/pytorch/captum.git torchscan num2words hiyapyco omgifol git+https://github.com/alex404/sample-factory.git@fix-vtrace dpcpp-cpp-rt seaborn hydra-core networkx
+
+  # install CI related dependencies
+  pip3 install pylint

From 6208c69ea20f70151e0fc4867347815ac52deed4 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Tue, 8 Oct 2024 11:00:32 +0200
Subject: [PATCH 02/49] fix: fixed pycairo version in singularity def file

---
 resources/retinal-rl.def | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/resources/retinal-rl.def b/resources/retinal-rl.def
index 71ca034..4f6ddf7 100644
--- a/resources/retinal-rl.def
+++ b/resources/retinal-rl.def
@@ -58,7 +58,7 @@ From: nvidia/cuda:11.7.1-runtime-ubuntu22.04
 
   # retinal-rl Extra
 
-  pip3 install gymnasium==0.28.1 torch==1.13.1 vizdoom==1.2.0 torchvision==0.14.1 matplotlib opentsne pygame pycairo git+https://github.com/pytorch/captum.git torchscan num2words hiyapyco omgifol git+https://github.com/alex404/sample-factory.git@fix-vtrace dpcpp-cpp-rt seaborn hydra-core networkx
+  pip3 install gymnasium==0.28.1 torch==1.13.1 vizdoom==1.2.0 torchvision==0.14.1 matplotlib opentsne pygame pycairo==1.26.1 git+https://github.com/pytorch/captum.git torchscan num2words hiyapyco omgifol git+https://github.com/alex404/sample-factory.git@fix-vtrace dpcpp-cpp-rt seaborn hydra-core networkx
 
   # install CI related dependencies
   pip3 install pylint

From d4840d8a2a06657fb3cade8b22099219e79b9ddb Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Tue, 8 Oct 2024 15:44:38 +0200
Subject: [PATCH 03/49] perf: reduce size of singularity container

---
 resources/retinal-rl.def | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/resources/retinal-rl.def b/resources/retinal-rl.def
index 4f6ddf7..c6be54a 100644
--- a/resources/retinal-rl.def
+++ b/resources/retinal-rl.def
@@ -58,7 +58,10 @@ From: nvidia/cuda:11.7.1-runtime-ubuntu22.04
 
   # retinal-rl Extra
 
-  pip3 install gymnasium==0.28.1 torch==1.13.1 vizdoom==1.2.0 torchvision==0.14.1 matplotlib opentsne pygame pycairo==1.26.1 git+https://github.com/pytorch/captum.git torchscan num2words hiyapyco omgifol git+https://github.com/alex404/sample-factory.git@fix-vtrace dpcpp-cpp-rt seaborn hydra-core networkx
-
-  # install CI related dependencies
-  pip3 install pylint
+  pip3 install --no-cache-dir gymnasium==0.28.1 torch==1.13.1 vizdoom==1.2.0 torchvision==0.14.1 matplotlib opentsne pygame pycairo==1.26.1 git+https://github.com/pytorch/captum.git torchscan num2words hiyapyco omgifol git+https://github.com/alex404/sample-factory.git@fix-vtrace dpcpp-cpp-rt seaborn hydra-core networkx pylint
+  
+  # Clean up for smaller container size
+  rm acc159linux-x64.zip
+  apt clean
+  rm -rf /var/lib/apt/lists/*
+  rm -rf /root/.cache/pip
\ No newline at end of file

From b57fbc15d2196215505fa011a993eeecdcb582a5 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Tue, 8 Oct 2024 15:58:34 +0200
Subject: [PATCH 04/49] fix: replace container build with pull

---
 .github/workflows/pylint.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
index c4e9c21..cb20372 100644
--- a/.github/workflows/pylint.yml
+++ b/.github/workflows/pylint.yml
@@ -11,8 +11,8 @@ jobs:
       with:
         apptainer-version: 1.3.0
 
-    - name: Build Singularity container
-      run: apptainer build retinal-rl.sif resources/retinal-rl.def
+    - name: Pulling Singularity container
+      run: singularity pull retinal-rl.sif library://fabioseel/retinal-rl/default
 
     - name: Run Pylint
       run: singularity exec retinal-rl.sif pylint $(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')

From 50940c751ffa2cafc329e3388acc4a2cd6abf961 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Tue, 8 Oct 2024 17:25:04 +0200
Subject: [PATCH 05/49] fix(?): move singularity image to github / ghcr.io

---
 .github/workflows/pylint.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
index cb20372..d3b7579 100644
--- a/.github/workflows/pylint.yml
+++ b/.github/workflows/pylint.yml
@@ -12,7 +12,7 @@ jobs:
         apptainer-version: 1.3.0
 
     - name: Pulling Singularity container
-      run: singularity pull retinal-rl.sif library://fabioseel/retinal-rl/default
+      run: singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-latest
 
     - name: Run Pylint
-      run: singularity exec retinal-rl.sif pylint $(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')
+      run: singularity exec retinal-rl_singularity-image-latest.sif pylint $(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')

From 1e2c6fa0eb5c8123d58e4bfcbc136b62d3147fea Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Tue, 8 Oct 2024 17:32:51 +0200
Subject: [PATCH 06/49] fix(?): add auto login credentials to workflow

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

diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
index d3b7579..5f79a69 100644
--- a/.github/workflows/pylint.yml
+++ b/.github/workflows/pylint.yml
@@ -12,7 +12,7 @@ jobs:
         apptainer-version: 1.3.0
 
     - name: Pulling Singularity container
-      run: singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-latest
+      run: singularity remote login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} ghcr.io; singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-latest
 
     - name: Run Pylint
       run: singularity exec retinal-rl_singularity-image-latest.sif pylint $(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')

From c5e133d0a746d3db69597e198fd5b3170e6c4f9b Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Tue, 8 Oct 2024 17:34:37 +0200
Subject: [PATCH 07/49] fix(?): try fixing the auto login

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

diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
index 5f79a69..475d26b 100644
--- a/.github/workflows/pylint.yml
+++ b/.github/workflows/pylint.yml
@@ -12,7 +12,7 @@ jobs:
         apptainer-version: 1.3.0
 
     - name: Pulling Singularity container
-      run: singularity remote login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} ghcr.io; singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-latest
+      run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io; singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-latest
 
     - name: Run Pylint
       run: singularity exec retinal-rl_singularity-image-latest.sif pylint $(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')

From 0fe89829957a1a9b5046e08a658bb62af4e5b84d Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Tue, 8 Oct 2024 17:38:25 +0200
Subject: [PATCH 08/49] fix(?): typo in package name for singularity container
 in workflow

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

diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
index 475d26b..3b30f4a 100644
--- a/.github/workflows/pylint.yml
+++ b/.github/workflows/pylint.yml
@@ -12,7 +12,7 @@ jobs:
         apptainer-version: 1.3.0
 
     - name: Pulling Singularity container
-      run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io; singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-latest
+      run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io; singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
 
     - name: Run Pylint
       run: singularity exec retinal-rl_singularity-image-latest.sif pylint $(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')

From e592feb55b2849cb3ca8a910eb0060e38a8cff6e Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Wed, 9 Oct 2024 09:58:24 +0200
Subject: [PATCH 09/49] fix(?): pylint to all files instead of just changed
 (for now)

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

diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
index 3b30f4a..ec2548d 100644
--- a/.github/workflows/pylint.yml
+++ b/.github/workflows/pylint.yml
@@ -15,4 +15,4 @@ jobs:
       run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io; singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
 
     - name: Run Pylint
-      run: singularity exec retinal-rl_singularity-image-latest.sif pylint $(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')
+      run: singularity exec retinal-rl_singularity-image-latest.sif pylint . #$(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')

From f7f9b49ba2d7da6085a95bf6a07625adf6bcaa42 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Wed, 9 Oct 2024 10:58:18 +0200
Subject: [PATCH 10/49] chore: try bumping checkout action version to v4

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

diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
index ec2548d..c63f94c 100644
--- a/.github/workflows/pylint.yml
+++ b/.github/workflows/pylint.yml
@@ -6,7 +6,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: eWaterCycle/setup-apptainer@v2
       with:
         apptainer-version: 1.3.0

From 550e0a197f78560f9ffdea607a4142a2b4d0e2f5 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Wed, 9 Oct 2024 14:46:28 +0200
Subject: [PATCH 11/49] fix: update example cfgs

---
 ...assifier.yaml => shallow-autoencoder.yaml} | 20 ++++----
 ...r10-large.yaml => cifar10-decontrast.yaml} |  6 +--
 .../user/experiment/cifar10-class-recon.yaml  | 29 ++++++------
 .../user/optimizer/class-recon.yaml           | 46 -------------------
 .../user/optimizer/recon-weight.yaml          | 45 ++++++++++++++++++
 5 files changed, 70 insertions(+), 76 deletions(-)
 rename resources/config_templates/user/brain/{retinal-classifier.yaml => shallow-autoencoder.yaml} (88%)
 rename resources/config_templates/user/dataset/{cifar10-large.yaml => cifar10-decontrast.yaml} (77%)
 delete mode 100644 resources/config_templates/user/optimizer/class-recon.yaml
 create mode 100644 resources/config_templates/user/optimizer/recon-weight.yaml

diff --git a/resources/config_templates/user/brain/retinal-classifier.yaml b/resources/config_templates/user/brain/shallow-autoencoder.yaml
similarity index 88%
rename from resources/config_templates/user/brain/retinal-classifier.yaml
rename to resources/config_templates/user/brain/shallow-autoencoder.yaml
index 1d65923..3cf4fc7 100644
--- a/resources/config_templates/user/brain/retinal-classifier.yaml
+++ b/resources/config_templates/user/brain/shallow-autoencoder.yaml
@@ -24,8 +24,8 @@ circuits:
     _target_: retinal_rl.models.circuits.convolutional.ConvolutionalEncoder
     num_layers: 2
     num_channels: [16,32]  # Two layers with 16 and 32 channels
-    kernel_size: ${kernel_size}
-    stride: ${stride}
+    kernel_size: 8
+    stride: 2
     act_name: ${activation}
     layer_names: ["bipolar", "retinal_ganglion"]  # Names inspired by retinal cell types
 
@@ -34,8 +34,8 @@ circuits:
     _target_: retinal_rl.models.circuits.convolutional.ConvolutionalEncoder
     num_layers: 1
     num_channels: 64
-    kernel_size: ${kernel_size}
-    stride: ${stride}
+    kernel_size: 5
+    stride: 1
     act_name: ${activation}
     layer_names: ["lgn"]  # Lateral Geniculate Nucleus
 
@@ -44,8 +44,8 @@ circuits:
     _target_: retinal_rl.models.circuits.convolutional.ConvolutionalEncoder
     num_layers: 1
     num_channels: 64
-    kernel_size: ${kernel_size}
-    stride: ${stride} 
+    kernel_size: 8
+    stride: 2
     act_name: ${activation}
     layer_names: ["v1"]  # Primary Visual Cortex
 
@@ -53,9 +53,9 @@ circuits:
   pfc:
     _target_: retinal_rl.models.circuits.fully_connected.FullyConnectedEncoder
     output_shape:
-      - ${latent_size}  # Size of the latent representation
+      - 128  # Size of the latent representation
     hidden_units: 
-      - ${hidden_units}  # Number of hidden units
+      - 64  # Number of hidden units
     act_name: ${activation}
 
   # Decoder: for reconstructing the input from the latent representation
@@ -63,8 +63,8 @@ circuits:
     _target_: retinal_rl.models.circuits.convolutional.ConvolutionalDecoder
     num_layers: 3
     num_channels: [32,16,3]  # For a symmetric encoder, this should be the reverse of the num_channels in the CNN layers up to the point of decoding (in this case, the thalamus)
-    kernel_size: ${kernel_size}
-    stride: ${stride}
+    kernel_size: [5,8,8]
+    stride: [1,2,2]
     act_name: ${activation}
 
   # Classifier: for categorizing the input into classes
diff --git a/resources/config_templates/user/dataset/cifar10-large.yaml b/resources/config_templates/user/dataset/cifar10-decontrast.yaml
similarity index 77%
rename from resources/config_templates/user/dataset/cifar10-large.yaml
rename to resources/config_templates/user/dataset/cifar10-decontrast.yaml
index 645607d..5e0624b 100644
--- a/resources/config_templates/user/dataset/cifar10-large.yaml
+++ b/resources/config_templates/user/dataset/cifar10-decontrast.yaml
@@ -11,11 +11,9 @@ imageset:
       image_rescale_range: [1, 5]
   noise_transforms:
     - _target_: retinal_rl.datasets.transforms.ShotNoiseTransform
-      lambda_range: [0.8, 1.2]
+      lambda_range: [0.5, 1.5]
     - _target_: retinal_rl.datasets.transforms.ContrastTransform
-      contrast_range: [0.5, 1.5]
+      contrast_range: [0.01, 1.2]
   apply_normalization: true
-  # normalization_mean: [0.4914, 0.4822, 0.4465]
-  # normalization_std: [0.2023, 0.1994, 0.2010]
   fixed_transformation: false
   multiplier: 1
diff --git a/resources/config_templates/user/experiment/cifar10-class-recon.yaml b/resources/config_templates/user/experiment/cifar10-class-recon.yaml
index fcc26de..3c1720c 100644
--- a/resources/config_templates/user/experiment/cifar10-class-recon.yaml
+++ b/resources/config_templates/user/experiment/cifar10-class-recon.yaml
@@ -1,25 +1,22 @@
-# This is the main entry point for users to specify their config parameters, and
-# should be freely copied and edited.
-
-# Defaults for the various subconfigs. Can be overriden from the commandline
-# with e.g. experiment/brain=new_brain, where new_brain.yaml lives in the brain
-# subdirectory
+# @package _global_
 defaults:
   - _self_
-  - sweep: kernel-size
-  - dataset: cifar10-large
-  - brain: retinal-classifier
-  - optimizer: class-recon
+  - override /dataset: cifar10-decontrast
+  - override /brain: shallow-autoencoder
+  - override /optimizer: recon-weight
 
-# This *must* match the experiment file name
-name: cifar10-class-recon
+# This is the main entry point for control of a retinal-rl experiment. Variables
+# created here will be top-level, and defaults can be set for the various parts
+# of an experiment (NB: do not add comments above the defaults list or it will
+# break the config system.)
 framework: classification
 
 # This is a free list of parameters that can be interpolated by the subconfigs
 # in sweep, dataset, brain, and optimizer. A major use for this is interpolating
 # values in the subconfigs, and then looping over them in a sweep.
-latent_size: 128
-hidden_units: 64
 activation: "elu"
-kernel_size: 8
-stride: 2
+activation_sparsity: 0.0001
+weight_decay: 0.0001
+sparse_objective: retinal_rl.models.objective.L1Sparsity
+recon_weight_retina: 1
+recon_weight_thalamus: 0.99
\ No newline at end of file
diff --git a/resources/config_templates/user/optimizer/class-recon.yaml b/resources/config_templates/user/optimizer/class-recon.yaml
deleted file mode 100644
index cdf8fc8..0000000
--- a/resources/config_templates/user/optimizer/class-recon.yaml
+++ /dev/null
@@ -1,46 +0,0 @@
-# BrainOptimizer config. Each top level defines a particular optimizer. Circuits
-# should appear in at most one optimizer.
-recon:
-  optimizer: # torch.optim Class and parameters
-    _target_: torch.optim.Adam
-    lr: 0.0003
-  min_epoch: 0 # Epoch to start optimizer
-  max_epoch: 100 # Epoch to stop optimizer
-  objectives: # Weighted optimizer objectives as defined in retinal-rl
-    - _target_: retinal_rl.models.objective.ReconstructionObjective
-      weight: 1
-    - _target_: retinal_rl.models.objective.L1Sparsity
-      weight: 0.001
-      target_responses:
-        - retina
-  target_circuits: # Circuit parameters to optimize with this optimizer.  We train the retina and the decoder exclusively to maximize reconstruction
-    - retina
-    - decoder
-mixed:
-  optimizer:
-    _target_: torch.optim.Adam
-    lr: 0.0003
-  min_epoch: 0
-  max_epoch: 100
-  objectives:
-    - _target_: retinal_rl.models.objective.ReconstructionObjective
-      weight: 0.99
-    - _target_: retinal_rl.classification.objective.ClassificationObjective
-      weight: 0.01
-  target_circuits: # The thalamus is somewhat sensitive to task objectives
-    - thalamus
-class:
-  optimizer:
-    _target_: torch.optim.Adam
-    lr: 0.0003
-  min_epoch: 0
-  max_epoch: 100
-  objectives:
-    - _target_: retinal_rl.classification.objective.ClassificationObjective
-      weight: 1
-    - _target_: retinal_rl.classification.objective.PercentCorrect
-      weight: 0
-  target_circuits: # Visual cortex and downstream layers are driven by the task
-    - visual_cortex
-    - pfc
-    - classifier
diff --git a/resources/config_templates/user/optimizer/recon-weight.yaml b/resources/config_templates/user/optimizer/recon-weight.yaml
new file mode 100644
index 0000000..83bc7e4
--- /dev/null
+++ b/resources/config_templates/user/optimizer/recon-weight.yaml
@@ -0,0 +1,45 @@
+optimizer: # torch.optim Class and parameters
+  _target_: torch.optim.Adam
+  lr: 0.0003
+
+goal:
+  recon:
+    min_epoch: 0 # Epoch to start optimizer
+    max_epoch: 100 # Epoch to stop optimizer
+    losses: # Weighted optimizer losses as defined in retinal-rl
+      - _target_: retinal_rl.models.loss.ReconstructionLoss
+        weight: ${recon_weight_retina}
+      - _target_: retinal_rl.classification.loss.ClassificationLoss
+        weight: ${eval:'1-${recon_weight_retina}'}
+    target_circuits: # Circuit parameters to optimize with this optimizer.  We train the retina and the decoder exclusively to maximize reconstruction
+      - retina
+  decode:
+    min_epoch: 0 # Epoch to start optimizer
+    max_epoch: 100 # Epoch to stop optimizer
+    losses: # Weighted optimizer losses as defined in retinal-rl
+      - _target_: retinal_rl.models.loss.ReconstructionLoss
+        weight: 1
+    target_circuits: # Circuit parameters to optimize with this optimizer.  We train the retina and the decoder exclusively to maximize reconstruction
+      - decoder
+  mixed:
+    min_epoch: 0
+    max_epoch: 100
+    losses:
+      - _target_: retinal_rl.models.loss.ReconstructionLoss
+        weight: ${recon_weight_thalamus}
+      - _target_: retinal_rl.classification.loss.ClassificationLoss
+        weight: ${eval:'1-${recon_weight_thalamus}'}
+    target_circuits: # The thalamus is somewhat sensitive to task losses
+      - thalamus
+  class:
+    min_epoch: 0
+    max_epoch: 100
+    losses:
+      - _target_: retinal_rl.classification.loss.ClassificationLoss
+        weight: 1
+      - _target_: retinal_rl.classification.loss.PercentCorrect
+        weight: 0
+    target_circuits: # Visual cortex and downstream layers are driven by the task
+      - visual_cortex
+      - pfc
+      - classifier

From 45ae1550d766574d5303448d48a70f56d93362e9 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Wed, 9 Oct 2024 14:48:05 +0200
Subject: [PATCH 12/49] fix: make pylint not fail the pipeline (WIP)

---
 .github/workflows/{pylint.yml => code_check.yml} | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)
 rename .github/workflows/{pylint.yml => code_check.yml} (81%)

diff --git a/.github/workflows/pylint.yml b/.github/workflows/code_check.yml
similarity index 81%
rename from .github/workflows/pylint.yml
rename to .github/workflows/code_check.yml
index c63f94c..4b4648c 100644
--- a/.github/workflows/pylint.yml
+++ b/.github/workflows/code_check.yml
@@ -1,4 +1,4 @@
-name: Pylint
+name: Code Checking
 
 on: [push, pull_request]
 
@@ -15,4 +15,4 @@ jobs:
       run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io; singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
 
     - name: Run Pylint
-      run: singularity exec retinal-rl_singularity-image-latest.sif pylint . #$(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')
+      run: singularity exec retinal-rl_singularity-image-latest.sif pylint --exit-zero . #$(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')

From 2180265853176008e723393567484831cba588e3 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Wed, 9 Oct 2024 14:48:24 +0200
Subject: [PATCH 13/49] feat: add workflow to check if cfgs can be read

---
 .github/workflows/config_scan.yaml | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 .github/workflows/config_scan.yaml

diff --git a/.github/workflows/config_scan.yaml b/.github/workflows/config_scan.yaml
new file mode 100644
index 0000000..ada1c47
--- /dev/null
+++ b/.github/workflows/config_scan.yaml
@@ -0,0 +1,21 @@
+name: Scan Configs
+
+on: [push, pull_request]
+
+jobs:
+  scan:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: eWaterCycle/setup-apptainer@v2
+      with:
+        apptainer-version: 1.3.0
+
+    - name: Pulling Singularity container
+      run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io; singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
+
+    - name: Copy configs from resources directory
+      run: cp -r resources/config_templates/user/* config/user/
+
+    - name: Scan classification config
+      run: singularity exec retinal-rl_singularity-image-latest.sif python main.py -m +experiment=cifar10-class-recon command=scan
\ No newline at end of file

From f2870ff6c8c4d19be766f5011c5f19539f9ed867 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Wed, 9 Oct 2024 14:51:42 +0200
Subject: [PATCH 14/49] fix: paths in config scan workflow

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

diff --git a/.github/workflows/config_scan.yaml b/.github/workflows/config_scan.yaml
index ada1c47..20c11c6 100644
--- a/.github/workflows/config_scan.yaml
+++ b/.github/workflows/config_scan.yaml
@@ -15,7 +15,7 @@ jobs:
       run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io; singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
 
     - name: Copy configs from resources directory
-      run: cp -r resources/config_templates/user/* config/user/
+      run: cp -r resources/config_templates/* config/
 
     - name: Scan classification config
       run: singularity exec retinal-rl_singularity-image-latest.sif python main.py -m +experiment=cifar10-class-recon command=scan
\ No newline at end of file

From 2da3900f30fb8f2d4faeec1c1d5098f35ecc62ce Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Wed, 9 Oct 2024 15:05:13 +0200
Subject: [PATCH 15/49] fix: make config scan run without cuda / gpu

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

diff --git a/.github/workflows/config_scan.yaml b/.github/workflows/config_scan.yaml
index 20c11c6..85fd3d0 100644
--- a/.github/workflows/config_scan.yaml
+++ b/.github/workflows/config_scan.yaml
@@ -18,4 +18,4 @@ jobs:
       run: cp -r resources/config_templates/* config/
 
     - name: Scan classification config
-      run: singularity exec retinal-rl_singularity-image-latest.sif python main.py -m +experiment=cifar10-class-recon command=scan
\ No newline at end of file
+      run: singularity exec retinal-rl_singularity-image-latest.sif python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file

From 84cc1fa74a916d93db1cb0b53f80c9d3bd9b6c49 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Wed, 9 Oct 2024 15:38:50 +0200
Subject: [PATCH 16/49] feat: add workflow to test whether singularity
 container can be build

---
 .../{config_scan.yaml => config_scan.yml}         |  0
 .github/workflows/container_build.yml             | 15 +++++++++++++++
 2 files changed, 15 insertions(+)
 rename .github/workflows/{config_scan.yaml => config_scan.yml} (100%)
 create mode 100644 .github/workflows/container_build.yml

diff --git a/.github/workflows/config_scan.yaml b/.github/workflows/config_scan.yml
similarity index 100%
rename from .github/workflows/config_scan.yaml
rename to .github/workflows/config_scan.yml
diff --git a/.github/workflows/container_build.yml b/.github/workflows/container_build.yml
new file mode 100644
index 0000000..3f57bd0
--- /dev/null
+++ b/.github/workflows/container_build.yml
@@ -0,0 +1,15 @@
+name: Build Singularity Container
+
+on: [push, pull_request]
+
+jobs:
+  singularity-build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: eWaterCycle/setup-apptainer@v2
+      with:
+        apptainer-version: 1.3.0
+
+    - name: Build Singularity container
+      run: apptainer build retinal-rl.sif resources/retinal-rl.def
\ No newline at end of file

From 361702a453872c3eeac6df19579b1a20bc0e2457 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Wed, 9 Oct 2024 16:38:04 +0200
Subject: [PATCH 17/49] feat: container build with automatical upload to ghcr

---
 .github/workflows/container_build.yml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/container_build.yml b/.github/workflows/container_build.yml
index 3f57bd0..2d7cb65 100644
--- a/.github/workflows/container_build.yml
+++ b/.github/workflows/container_build.yml
@@ -6,10 +6,16 @@ jobs:
   singularity-build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: eWaterCycle/setup-apptainer@v2
       with:
         apptainer-version: 1.3.0
 
     - name: Build Singularity container
-      run: apptainer build retinal-rl.sif resources/retinal-rl.def
\ No newline at end of file
+      run: apptainer build retinal-rl.sif resources/retinal-rl.def
+
+    - name: Scan classification config / ensure minimal functionality
+      run: singularity exec retinal-rl_singularity-image-latest.sif python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
+
+    - name: Push to ghcr.io
+      run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io; singularity push retinal-rl.sif oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
\ No newline at end of file

From 5c53f589015a817f7ad4705492f57cf9e6b503bf Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Wed, 9 Oct 2024 16:49:59 +0200
Subject: [PATCH 18/49] fix: name of created sif file for scan

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

diff --git a/.github/workflows/container_build.yml b/.github/workflows/container_build.yml
index 2d7cb65..ae10ca7 100644
--- a/.github/workflows/container_build.yml
+++ b/.github/workflows/container_build.yml
@@ -15,7 +15,7 @@ jobs:
       run: apptainer build retinal-rl.sif resources/retinal-rl.def
 
     - name: Scan classification config / ensure minimal functionality
-      run: singularity exec retinal-rl_singularity-image-latest.sif python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
+      run: singularity exec retinal-rl.sif python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
 
     - name: Push to ghcr.io
       run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io; singularity push retinal-rl.sif oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
\ No newline at end of file

From e9d52ec6b084010f8f60f6a211b3a05d32645401 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 11:08:26 +0200
Subject: [PATCH 19/49] fix/refactor: build and push now should run, nicify
 multiline comments, test reusable workflows

---
 .github/workflows/code_check.yml       |  4 +++-
 .github/workflows/config_scan.yml      | 22 +++++---------------
 .github/workflows/container_build.yml  |  8 ++++++--
 .github/workflows/singularity_pull.yml | 28 ++++++++++++++++++++++++++
 4 files changed, 42 insertions(+), 20 deletions(-)
 create mode 100644 .github/workflows/singularity_pull.yml

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 4b4648c..8f92a8a 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -12,7 +12,9 @@ jobs:
         apptainer-version: 1.3.0
 
     - name: Pulling Singularity container
-      run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io; singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
+      run: |
+        singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
+        singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
 
     - name: Run Pylint
       run: singularity exec retinal-rl_singularity-image-latest.sif pylint --exit-zero . #$(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 85fd3d0..82b08d2 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -1,21 +1,9 @@
 name: Scan Configs
-
 on: [push, pull_request]
-
 jobs:
   scan:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - uses: eWaterCycle/setup-apptainer@v2
-      with:
-        apptainer-version: 1.3.0
-
-    - name: Pulling Singularity container
-      run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io; singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
-
-    - name: Copy configs from resources directory
-      run: cp -r resources/config_templates/* config/
-
-    - name: Scan classification config
-      run: singularity exec retinal-rl_singularity-image-latest.sif python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file
+    uses: ./.github/workflows/singularity_pull.yml
+    with:
+      singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
+    secrets:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
\ No newline at end of file
diff --git a/.github/workflows/container_build.yml b/.github/workflows/container_build.yml
index ae10ca7..94d9690 100644
--- a/.github/workflows/container_build.yml
+++ b/.github/workflows/container_build.yml
@@ -15,7 +15,11 @@ jobs:
       run: apptainer build retinal-rl.sif resources/retinal-rl.def
 
     - name: Scan classification config / ensure minimal functionality
-      run: singularity exec retinal-rl.sif python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
+      run: |
+        cp -r resources/config_templates/* config/
+        singularity exec retinal-rl.sif python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
 
     - name: Push to ghcr.io
-      run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io; singularity push retinal-rl.sif oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
\ No newline at end of file
+      run: |
+        singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
+        singularity push retinal-rl.sif oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
\ No newline at end of file
diff --git a/.github/workflows/singularity_pull.yml b/.github/workflows/singularity_pull.yml
new file mode 100644
index 0000000..ef9ec28
--- /dev/null
+++ b/.github/workflows/singularity_pull.yml
@@ -0,0 +1,28 @@
+name: Reusable Pull and Scan
+
+on:
+  workflow_call:
+    inputs:
+      singularity_image:
+        required: true
+        type: string
+    secrets:
+      GITHUB_TOKEN:
+        required: true
+
+jobs:
+  reusable_job:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.3.0
+      - name: Login to ghcr
+        run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
+      - name: Pull Image
+        run: singularity pull ${{ inputs.singularity_image }}
+      - name: Scan classification config
+        run: |
+          cp -r resources/config_templates/* config/
+          singularity exec $(basename ${{ inputs.singularity_image }}) python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file

From 5d5985032c34c80e71014bac4e83f257b44b73c4 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 11:10:53 +0200
Subject: [PATCH 20/49] fix(?): reusable workflow

---
 .github/workflows/config_scan.yml      | 4 +---
 .github/workflows/singularity_pull.yml | 3 ---
 2 files changed, 1 insertion(+), 6 deletions(-)

diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 82b08d2..0002276 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -4,6 +4,4 @@ jobs:
   scan:
     uses: ./.github/workflows/singularity_pull.yml
     with:
-      singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
-    secrets:
-      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
\ No newline at end of file
+      singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
\ No newline at end of file
diff --git a/.github/workflows/singularity_pull.yml b/.github/workflows/singularity_pull.yml
index ef9ec28..bdbe05c 100644
--- a/.github/workflows/singularity_pull.yml
+++ b/.github/workflows/singularity_pull.yml
@@ -6,9 +6,6 @@ on:
       singularity_image:
         required: true
         type: string
-    secrets:
-      GITHUB_TOKEN:
-        required: true
 
 jobs:
   reusable_job:

From 8d848c26d8345de68d2631b378775c861dbf687f Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 11:26:41 +0200
Subject: [PATCH 21/49] fix(?):automatic referencing of sif file in reusable
 job

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

diff --git a/.github/workflows/singularity_pull.yml b/.github/workflows/singularity_pull.yml
index bdbe05c..cc04b48 100644
--- a/.github/workflows/singularity_pull.yml
+++ b/.github/workflows/singularity_pull.yml
@@ -22,4 +22,6 @@ jobs:
       - name: Scan classification config
         run: |
           cp -r resources/config_templates/* config/
-          singularity exec $(basename ${{ inputs.singularity_image }}) python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file
+          IMAGE_NAME=$(basename ${{ inputs.singularity_image }})
+          SIF_FILE="${IMAGE_NAME/:/_}.sif"
+          singularity exec $SIF_FILE python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file

From 453d8e3ba0703e69de61969ea80f5881e23e2540 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 11:57:03 +0200
Subject: [PATCH 22/49] feat: run build action once a month or when def file
 has changed

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

diff --git a/.github/workflows/container_build.yml b/.github/workflows/container_build.yml
index 94d9690..07760db 100644
--- a/.github/workflows/container_build.yml
+++ b/.github/workflows/container_build.yml
@@ -1,6 +1,11 @@
 name: Build Singularity Container
 
-on: [push, pull_request]
+on: 
+  schedule:
+    - cron: '0 2 1 * *'
+  push:
+    paths:
+      - 'resources/retinal-rl.def'
 
 jobs:
   singularity-build:

From 3352e36dda2943545246e4be796d51168a5c0b3a Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 12:01:05 +0200
Subject: [PATCH 23/49] refactor: adjust when code check and scan are run

---
 .github/workflows/code_check.yml  | 8 +++++++-
 .github/workflows/config_scan.yml | 2 +-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 8f92a8a..ef2ab01 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -1,6 +1,12 @@
 name: Code Checking
 
-on: [push, pull_request]
+on: 
+  push:
+    paths:
+      - '**/*.py'
+  pull_request:
+    branches:
+      - main
 
 jobs:
   lint:
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 0002276..fb3df25 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -1,5 +1,5 @@
 name: Scan Configs
-on: [push, pull_request]
+on: [pull_request,workflow_dispatch]
 jobs:
   scan:
     uses: ./.github/workflows/singularity_pull.yml

From 45b1928f7932f7051d538a2db744eebb91d10c88 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 13:54:31 +0200
Subject: [PATCH 24/49] feat: run pylint on changed py files (compared to
 master)

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

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index ef2ab01..f06711f 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -23,4 +23,4 @@ jobs:
         singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
 
     - name: Run Pylint
-      run: singularity exec retinal-rl_singularity-image-latest.sif pylint --exit-zero . #$(git diff --name-only origin/master origin/feat-ci-pipeline -- '*.py')
+      run: singularity exec retinal-rl_singularity-image-latest.sif pylint $(git diff --name-only origin/master HEAD -- '*.py')

From b26d636fa1a06ce3afb85168f99f8d259d3e12c2 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 14:09:35 +0200
Subject: [PATCH 25/49] refactor: reusable action for initial setup

---
 .github/workflows/code_check.yml                 | 14 ++++++++------
 .github/workflows/config_scan.yml                | 16 +++++++++++++---
 .../{singularity_pull.yml => setup.yml}          | 12 ++++--------
 3 files changed, 25 insertions(+), 17 deletions(-)
 rename .github/workflows/{singularity_pull.yml => setup.yml} (57%)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index f06711f..ceb2b34 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -8,6 +8,10 @@ on:
     branches:
       - main
 
+env:
+  singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
+  sif_file: retinal-rl_singularity-image-latest.sif
+
 jobs:
   lint:
     runs-on: ubuntu-latest
@@ -16,11 +20,9 @@ jobs:
     - uses: eWaterCycle/setup-apptainer@v2
       with:
         apptainer-version: 1.3.0
-
-    - name: Pulling Singularity container
-      run: |
-        singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
-        singularity pull oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
+    - uses: ./.github/workflows/setup.yml
+      with:
+        singularity_image: ${{ env.singularity_image }}
 
     - name: Run Pylint
-      run: singularity exec retinal-rl_singularity-image-latest.sif pylint $(git diff --name-only origin/master HEAD -- '*.py')
+      run: singularity exec ${{ env.sif_file }} pylint $(git diff --name-only origin/master HEAD -- '*.py')
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index fb3df25..9764101 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -1,7 +1,17 @@
 name: Scan Configs
 on: [pull_request,workflow_dispatch]
+
+env:
+  singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
+  sif_file: retinal-rl_singularity-image-latest.sif
+
 jobs:
   scan:
-    uses: ./.github/workflows/singularity_pull.yml
-    with:
-      singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
\ No newline at end of file
+    runs-on: ubuntu-latest
+    steps:
+    - uses: ./.github/workflows/setup.yml
+      with:
+        singularity_image: ${{ env.singularity_image }}
+
+    - name: Scan classification config
+      run: singularity exec ${{ env.sif_file }} python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file
diff --git a/.github/workflows/singularity_pull.yml b/.github/workflows/setup.yml
similarity index 57%
rename from .github/workflows/singularity_pull.yml
rename to .github/workflows/setup.yml
index cc04b48..d387e3e 100644
--- a/.github/workflows/singularity_pull.yml
+++ b/.github/workflows/setup.yml
@@ -1,4 +1,4 @@
-name: Reusable Pull and Scan
+name: Pull Singularity container & Setup Repository
 
 on:
   workflow_call:
@@ -8,7 +8,7 @@ on:
         type: string
 
 jobs:
-  reusable_job:
+  setup:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -19,9 +19,5 @@ jobs:
         run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
       - name: Pull Image
         run: singularity pull ${{ inputs.singularity_image }}
-      - name: Scan classification config
-        run: |
-          cp -r resources/config_templates/* config/
-          IMAGE_NAME=$(basename ${{ inputs.singularity_image }})
-          SIF_FILE="${IMAGE_NAME/:/_}.sif"
-          singularity exec $SIF_FILE python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file
+      - name: Copy Configs
+        run: cp -r resources/config_templates/* config/
\ No newline at end of file

From 1d65f0ec7c770e06444d775cf9cecfe94fd1ce39 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 14:10:37 +0200
Subject: [PATCH 26/49] fix: pylint complains in compile scenario of
 doom_creator

---
 ...ompile-scenario.py => compile_scenario.py} | 34 +++++++++++++++++--
 1 file changed, 31 insertions(+), 3 deletions(-)
 rename doom_creator/{compile-scenario.py => compile_scenario.py} (77%)

diff --git a/doom_creator/compile-scenario.py b/doom_creator/compile_scenario.py
similarity index 77%
rename from doom_creator/compile-scenario.py
rename to doom_creator/compile_scenario.py
index d6450ea..395531c 100644
--- a/doom_creator/compile-scenario.py
+++ b/doom_creator/compile_scenario.py
@@ -1,3 +1,15 @@
+"""Scenario Compiler for Retinal-RL
+
+This module provides a utility to construct scenarios for the retinal-rl project.
+It merges YAML files from a specified directory into a scenario specification and
+subsequently compiles the scenario defined through those yaml files.
+
+Usage:
+    python -m exec.compile-scenario [options] [yaml_files...]
+
+Example:
+    python -m exec.compile-scenario gathering apples"""
+
 import argparse
 import os
 import sys
@@ -11,6 +23,13 @@
 
 
 def make_parser():
+    """
+    Create and configure an argument parser for the scenario compiler.
+    Check the parsers description and arguments help for further information.
+
+    Returns:
+        argparse.ArgumentParser: Configured argument parser for the scenario compiler.
+    """
     # Initialize parser
     Directories()
     parser = argparse.ArgumentParser(
@@ -22,7 +41,7 @@ def make_parser():
         running the first time one should use the --preload flag to download the
         necessary resources into the --out_dir ('{Directories().CACHE_DIR}').
         """,
-        epilog="Example: python -m exec.compile-scenario gathering apples",
+        epilog="Example: python -m exec.compile_scenario gathering apples",
     )
     # Positional argument for scenario yaml files (required, can be multiple)
     parser.add_argument(
@@ -44,7 +63,7 @@ def make_parser():
     parser.add_argument(
         "--dataset_dir",
         default=None,
-        help="source directory of a dataset (for preloading), if you already downloaded it somewhere",
+        help="source directory of a dataset (for preloading), if already downloaded somewhere",
     )
     parser.add_argument(
         "--resource_dir",
@@ -72,6 +91,15 @@ def make_parser():
 
 
 def main():
+    """
+    Main function to parse arguments and execute scenario compilation tasks.
+    
+    The function supports various modes of operation including preloading resources,
+    listing available YAML files, and creating scenarios. It also handles error
+    checking and warns the user if no actions are specified.
+
+    For a more detailed documentation, check the parser.
+    """
     # Parse args
     argv = sys.argv[1:]
     parser = make_parser()
@@ -92,7 +120,7 @@ def main():
         print(f"Listing contents of {dirs.SCENARIO_YAML_DIR}:")
         for flnm in os.listdir(dirs.SCENARIO_YAML_DIR):
             print(flnm)
-        print(f"If you want to load from a different folder, change this to")
+        print("If you want to load from a different folder, change this to")
     if do_make:
         cfg, needed_types = check_preload(cfg, args.test)
         any_dataset = False

From 9522e10009852c5096ce777441ced190fd5a9562 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 14:15:37 +0200
Subject: [PATCH 27/49] fix: checkout must be in every top level workflow

---
 .github/workflows/code_check.yml  | 7 ++-----
 .github/workflows/config_scan.yml | 1 +
 .github/workflows/setup.yml       | 1 -
 3 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index ceb2b34..19ed202 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -2,8 +2,8 @@ name: Code Checking
 
 on: 
   push:
-    paths:
-      - '**/*.py'
+    # paths:
+    #   - '**/*.py'
   pull_request:
     branches:
       - main
@@ -17,9 +17,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - uses: eWaterCycle/setup-apptainer@v2
-      with:
-        apptainer-version: 1.3.0
     - uses: ./.github/workflows/setup.yml
       with:
         singularity_image: ${{ env.singularity_image }}
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 9764101..5fb1e81 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -9,6 +9,7 @@ jobs:
   scan:
     runs-on: ubuntu-latest
     steps:
+    - uses: actions/checkout@v4
     - uses: ./.github/workflows/setup.yml
       with:
         singularity_image: ${{ env.singularity_image }}
diff --git a/.github/workflows/setup.yml b/.github/workflows/setup.yml
index d387e3e..439d67b 100644
--- a/.github/workflows/setup.yml
+++ b/.github/workflows/setup.yml
@@ -11,7 +11,6 @@ jobs:
   setup:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
       - uses: eWaterCycle/setup-apptainer@v2
         with:
           apptainer-version: 1.3.0

From 19ecf45da24b6f60c7d68d3707e7869ac0d4d88c Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 14:17:08 +0200
Subject: [PATCH 28/49] fix(?): add checkout also to setup workflow

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

diff --git a/.github/workflows/setup.yml b/.github/workflows/setup.yml
index 439d67b..d387e3e 100644
--- a/.github/workflows/setup.yml
+++ b/.github/workflows/setup.yml
@@ -11,6 +11,7 @@ jobs:
   setup:
     runs-on: ubuntu-latest
     steps:
+      - uses: actions/checkout@v4
       - uses: eWaterCycle/setup-apptainer@v2
         with:
           apptainer-version: 1.3.0

From 00dddfd987688b9506b71cdfce76fbaf3357e067 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 14:36:48 +0200
Subject: [PATCH 29/49] fix(?): reusable workflow

---
 .github/workflows/code_check.yml  | 7 +++++--
 .github/workflows/config_scan.yml | 7 +++++--
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 19ed202..3e86a17 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -13,13 +13,16 @@ env:
   sif_file: retinal-rl_singularity-image-latest.sif
 
 jobs:
-  lint:
+  init:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
     - uses: ./.github/workflows/setup.yml
       with:
         singularity_image: ${{ env.singularity_image }}
 
+  lint:
+    needs: init
+    runs-on: ubuntu-latest
+    steps:
     - name: Run Pylint
       run: singularity exec ${{ env.sif_file }} pylint $(git diff --name-only origin/master HEAD -- '*.py')
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 5fb1e81..af21d8c 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -6,13 +6,16 @@ env:
   sif_file: retinal-rl_singularity-image-latest.sif
 
 jobs:
-  scan:
+  init:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
     - uses: ./.github/workflows/setup.yml
       with:
         singularity_image: ${{ env.singularity_image }}
 
+  scan:
+    needs: init
+    runs-on: ubuntu-latest
+    steps:
     - name: Scan classification config
       run: singularity exec ${{ env.sif_file }} python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file

From 2840e462e8bce837587212cb202d7431064615ad Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 14:40:35 +0200
Subject: [PATCH 30/49] fix(?): local workflows can not be called in steps

---
 .github/workflows/code_check.yml  | 8 +++-----
 .github/workflows/config_scan.yml | 8 +++-----
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 3e86a17..330fbc9 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -14,11 +14,9 @@ env:
 
 jobs:
   init:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: ./.github/workflows/setup.yml
-      with:
-        singularity_image: ${{ env.singularity_image }}
+    uses: ./.github/workflows/setup.yml
+    with:
+      singularity_image: ${{ env.singularity_image }}
 
   lint:
     needs: init
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index af21d8c..ac4d25d 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -7,11 +7,9 @@ env:
 
 jobs:
   init:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: ./.github/workflows/setup.yml
-      with:
-        singularity_image: ${{ env.singularity_image }}
+    uses: ./.github/workflows/setup.yml
+    with:
+      singularity_image: ${{ env.singularity_image }}
 
   scan:
     needs: init

From 70229c369927314be6b00de0437ba877d57878d5 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 14:53:12 +0200
Subject: [PATCH 31/49] fix: env variables seem poorly supported, removed that

---
 .github/workflows/code_check.yml  | 8 ++------
 .github/workflows/config_scan.yml | 8 ++------
 2 files changed, 4 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 330fbc9..dc58d4d 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -8,19 +8,15 @@ on:
     branches:
       - main
 
-env:
-  singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
-  sif_file: retinal-rl_singularity-image-latest.sif
-
 jobs:
   init:
     uses: ./.github/workflows/setup.yml
     with:
-      singularity_image: ${{ env.singularity_image }}
+      singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
 
   lint:
     needs: init
     runs-on: ubuntu-latest
     steps:
     - name: Run Pylint
-      run: singularity exec ${{ env.sif_file }} pylint $(git diff --name-only origin/master HEAD -- '*.py')
+      run: singularity exec retinal-rl_singularity-image-latest.sif pylint $(git diff --name-only origin/master HEAD -- '*.py')
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index ac4d25d..8f7affd 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -1,19 +1,15 @@
 name: Scan Configs
 on: [pull_request,workflow_dispatch]
 
-env:
-  singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
-  sif_file: retinal-rl_singularity-image-latest.sif
-
 jobs:
   init:
     uses: ./.github/workflows/setup.yml
     with:
-      singularity_image: ${{ env.singularity_image }}
+      singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
 
   scan:
     needs: init
     runs-on: ubuntu-latest
     steps:
     - name: Scan classification config
-      run: singularity exec ${{ env.sif_file }} python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file
+      run: singularity exec retinal-rl_singularity-image-latest.sif python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file

From 40a09a81ca43bcd22b183f4764674a5230956225 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 15:11:08 +0200
Subject: [PATCH 32/49] feat: add cache, make code check more verbose

---
 .github/workflows/code_check.yml  | 10 +++++++++-
 .github/workflows/config_scan.yml |  5 ++++-
 .github/workflows/setup.yml       | 33 ++++++++++++++++++++++---------
 3 files changed, 37 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index dc58d4d..cfdaa77 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -13,10 +13,18 @@ jobs:
     uses: ./.github/workflows/setup.yml
     with:
       singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
+      sif_file: retinal-rl_singularity-image-latest.sif
 
   lint:
     needs: init
     runs-on: ubuntu-latest
     steps:
+    - name: list directory
+      run: ls
+    - uses: actions/checkout@v4
+    - name: list directory
+      run: ls
     - name: Run Pylint
-      run: singularity exec retinal-rl_singularity-image-latest.sif pylint $(git diff --name-only origin/master HEAD -- '*.py')
+      run: |
+        singularity exec ~/singularity_images/retinal-rl_singularity-image-latest.sif \
+        pylint $(git diff --name-only origin/master HEAD -- '*.py')
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 8f7affd..630fa5b 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -6,10 +6,13 @@ jobs:
     uses: ./.github/workflows/setup.yml
     with:
       singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
+      sif_file: retinal-rl_singularity-image-latest.sif
 
   scan:
     needs: init
     runs-on: ubuntu-latest
     steps:
     - name: Scan classification config
-      run: singularity exec retinal-rl_singularity-image-latest.sif python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file
+      run: |
+        singularity exec ~/singularity_images/retinal-rl_singularity-image-latest.sif \
+        python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file
diff --git a/.github/workflows/setup.yml b/.github/workflows/setup.yml
index d387e3e..efdc217 100644
--- a/.github/workflows/setup.yml
+++ b/.github/workflows/setup.yml
@@ -6,18 +6,33 @@ on:
       singularity_image:
         required: true
         type: string
+      sif_file:
+        required: true
+        type: string
 
 jobs:
-  setup:
+  init:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: eWaterCycle/setup-apptainer@v2
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      
+      - name: Setup Apptainer
+        uses: eWaterCycle/setup-apptainer@v2
         with:
           apptainer-version: 1.3.0
-      - name: Login to ghcr
-        run: singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
-      - name: Pull Image
-        run: singularity pull ${{ inputs.singularity_image }}
-      - name: Copy Configs
-        run: cp -r resources/config_templates/* config/
\ No newline at end of file
+      
+      - name: Cache Singularity Image
+        id: cache-singularity
+        uses: actions/cache@v3
+        with:
+          path: ~/singularity_images
+          key: ${{ runner.os }}-singularity-${{ hashFiles('**/singularity_image_url.txt') }}
+      
+      - name: Pull Singularity container
+        if: steps.cache-singularity.outputs.cache-hit != 'true'
+        run: |
+          mkdir -p ~/singularity_images
+          singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
+          singularity pull --dir ~/singularity_images ${{ inputs.sif_file }} ${{ inputs.singularity_image }}
+          echo "${{ inputs.singularity_image }}" > ~/singularity_images/singularity_image_url.txt
\ No newline at end of file

From 77f3121a81c425bbb259579644a86ab1321b2e1c Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 15:25:35 +0200
Subject: [PATCH 33/49] fix(?): code check comparison to master make init/get
 singularity action do only the caching/pulling

---
 .github/workflows/code_check.yml                  | 15 ++++++++-------
 .github/workflows/config_scan.yml                 |  4 +++-
 .../workflows/{setup.yml => get_singularity.yml}  |  7 ++-----
 3 files changed, 13 insertions(+), 13 deletions(-)
 rename .github/workflows/{setup.yml => get_singularity.yml} (88%)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index cfdaa77..f826811 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -10,7 +10,7 @@ on:
 
 jobs:
   init:
-    uses: ./.github/workflows/setup.yml
+    uses: ./.github/workflows/get_singularity.yml
     with:
       singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
       sif_file: retinal-rl_singularity-image-latest.sif
@@ -19,12 +19,13 @@ jobs:
     needs: init
     runs-on: ubuntu-latest
     steps:
-    - name: list directory
-      run: ls
-    - uses: actions/checkout@v4
-    - name: list directory
-      run: ls
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Fetch all branches
+      run: git fetch --all
     - name: Run Pylint
       run: |
         singularity exec ~/singularity_images/retinal-rl_singularity-image-latest.sif \
-        pylint $(git diff --name-only origin/master HEAD -- '*.py')
+        pylint $(git diff --name-only origin/master...HEAD -- '*.py')
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 630fa5b..51e5df4 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -3,7 +3,7 @@ on: [pull_request,workflow_dispatch]
 
 jobs:
   init:
-    uses: ./.github/workflows/setup.yml
+    uses: ./.github/workflows/get_singularity.yml
     with:
       singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
       sif_file: retinal-rl_singularity-image-latest.sif
@@ -12,7 +12,9 @@ jobs:
     needs: init
     runs-on: ubuntu-latest
     steps:
+    - uses: actions/checkout@v4
     - name: Scan classification config
       run: |
+        cp -r resources/config_templates/* config/
         singularity exec ~/singularity_images/retinal-rl_singularity-image-latest.sif \
         python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file
diff --git a/.github/workflows/setup.yml b/.github/workflows/get_singularity.yml
similarity index 88%
rename from .github/workflows/setup.yml
rename to .github/workflows/get_singularity.yml
index efdc217..411548e 100644
--- a/.github/workflows/setup.yml
+++ b/.github/workflows/get_singularity.yml
@@ -1,4 +1,4 @@
-name: Pull Singularity container & Setup Repository
+name: Get Singularity Container
 
 on:
   workflow_call:
@@ -13,10 +13,7 @@ on:
 jobs:
   init:
     runs-on: ubuntu-latest
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-      
+    steps:      
       - name: Setup Apptainer
         uses: eWaterCycle/setup-apptainer@v2
         with:

From e8fd44d061aa21c8812b27f1d2d5c3953b29894a Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 16:07:09 +0200
Subject: [PATCH 34/49] fix: screw reusable actions, hopefully it runs now

---
 .github/workflows/code_check.yml      | 30 +++++++++++++++++------
 .github/workflows/config_scan.yml     | 27 +++++++++++++++------
 .github/workflows/get_singularity.yml | 35 ---------------------------
 3 files changed, 42 insertions(+), 50 deletions(-)
 delete mode 100644 .github/workflows/get_singularity.yml

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index f826811..3c61a87 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -8,17 +8,31 @@ on:
     branches:
       - main
 
-jobs:
-  init:
-    uses: ./.github/workflows/get_singularity.yml
-    with:
-      singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
-      sif_file: retinal-rl_singularity-image-latest.sif
+env:
+  singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
+  sif_file: retinal-rl_singularity-image-latest.sif
 
-  lint:
-    needs: init
+jobs:
+  check:
     runs-on: ubuntu-latest
     steps:
+    - name: Setup Apptainer
+      uses: eWaterCycle/setup-apptainer@v2
+      with:
+        apptainer-version: 1.3.0
+    - name: Cache Singularity Image
+      id: cache-singularity
+      uses: actions/cache@v3
+      with:
+        path: ~/${{ env.sif_file }}
+        key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
+    - name: Pull Singularity container
+      if: steps.cache-singularity.outputs.cache-hit != 'true'
+      run: |
+        singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
+        singularity pull ${{ env.sif_file }} ${{ env.singularity_image }}
+
+
     - name: Checkout code
       uses: actions/checkout@v4
       with:
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 51e5df4..2978c3c 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -1,17 +1,30 @@
 name: Scan Configs
 on: [pull_request,workflow_dispatch]
 
-jobs:
-  init:
-    uses: ./.github/workflows/get_singularity.yml
-    with:
-      singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
-      sif_file: retinal-rl_singularity-image-latest.sif
+env:
+  singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest
+  sif_file: retinal-rl_singularity-image-latest.sif
 
+jobs:
   scan:
-    needs: init
     runs-on: ubuntu-latest
     steps:
+    - name: Setup Apptainer
+      uses: eWaterCycle/setup-apptainer@v2
+      with:
+        apptainer-version: 1.3.0
+    - name: Cache Singularity Image
+      id: cache-singularity
+      uses: actions/cache@v3
+      with:
+        path: ~/${{ env.sif_file }}
+        key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
+    - name: Pull Singularity container
+      if: steps.cache-singularity.outputs.cache-hit != 'true'
+      run: |
+        singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
+        singularity pull ${{ env.sif_file }} ${{ env.singularity_image }}
+
     - uses: actions/checkout@v4
     - name: Scan classification config
       run: |
diff --git a/.github/workflows/get_singularity.yml b/.github/workflows/get_singularity.yml
deleted file mode 100644
index 411548e..0000000
--- a/.github/workflows/get_singularity.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-name: Get Singularity Container
-
-on:
-  workflow_call:
-    inputs:
-      singularity_image:
-        required: true
-        type: string
-      sif_file:
-        required: true
-        type: string
-
-jobs:
-  init:
-    runs-on: ubuntu-latest
-    steps:      
-      - name: Setup Apptainer
-        uses: eWaterCycle/setup-apptainer@v2
-        with:
-          apptainer-version: 1.3.0
-      
-      - name: Cache Singularity Image
-        id: cache-singularity
-        uses: actions/cache@v3
-        with:
-          path: ~/singularity_images
-          key: ${{ runner.os }}-singularity-${{ hashFiles('**/singularity_image_url.txt') }}
-      
-      - name: Pull Singularity container
-        if: steps.cache-singularity.outputs.cache-hit != 'true'
-        run: |
-          mkdir -p ~/singularity_images
-          singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
-          singularity pull --dir ~/singularity_images ${{ inputs.sif_file }} ${{ inputs.singularity_image }}
-          echo "${{ inputs.singularity_image }}" > ~/singularity_images/singularity_image_url.txt
\ No newline at end of file

From ff58590c4fbb4054a03de66704984d2d5c75f6c6 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 16:09:32 +0200
Subject: [PATCH 35/49] fix: changed sif file path

---
 .github/workflows/code_check.yml  | 2 +-
 .github/workflows/config_scan.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 3c61a87..329612c 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -41,5 +41,5 @@ jobs:
       run: git fetch --all
     - name: Run Pylint
       run: |
-        singularity exec ~/singularity_images/retinal-rl_singularity-image-latest.sif \
+        singularity exec ${{ env.sif_file }} \
         pylint $(git diff --name-only origin/master...HEAD -- '*.py')
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 2978c3c..45afddc 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -29,5 +29,5 @@ jobs:
     - name: Scan classification config
       run: |
         cp -r resources/config_templates/* config/
-        singularity exec ~/singularity_images/retinal-rl_singularity-image-latest.sif \
+        singularity exec ${{ env.sif_file }} \
         python main.py -m +experiment=cifar10-class-recon command=scan system.device=cpu
\ No newline at end of file

From 17db57ecf26540540d5ea89b37803badbf038b4f Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 16:18:56 +0200
Subject: [PATCH 36/49] exp: show state of directory before / after checkout

---
 .github/workflows/code_check.yml | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 329612c..ad3cb74 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -32,14 +32,21 @@ jobs:
         singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
         singularity pull ${{ env.sif_file }} ${{ env.singularity_image }}
 
-
+    - name: List current state
+      run: | 
+        ls
+        pwd
     - name: Checkout code
       uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Fetch all branches
       run: git fetch --all
-    - name: Run Pylint
-      run: |
-        singularity exec ${{ env.sif_file }} \
-        pylint $(git diff --name-only origin/master...HEAD -- '*.py')
+    - name: List current state
+      run: | 
+        ls
+        pwd
+    # - name: Run Pylint
+    #   run: |
+    #     singularity exec ${{ env.sif_file }} \
+    #     pylint $(git diff --name-only origin/master...HEAD -- '*.py')

From 298af6d020cdd85c1b83ae4a7cd1548266640fff Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 16:22:29 +0200
Subject: [PATCH 37/49] fix(?): checkout first before pulling container

---
 .github/workflows/code_check.yml | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index ad3cb74..082be82 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -16,6 +16,17 @@ jobs:
   check:
     runs-on: ubuntu-latest
     steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Fetch all branches
+      run: git fetch --all
+
+    - name: List current state
+      run: | 
+        ls
+        pwd
     - name: Setup Apptainer
       uses: eWaterCycle/setup-apptainer@v2
       with:
@@ -31,17 +42,7 @@ jobs:
       run: |
         singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
         singularity pull ${{ env.sif_file }} ${{ env.singularity_image }}
-
-    - name: List current state
-      run: | 
-        ls
-        pwd
-    - name: Checkout code
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-    - name: Fetch all branches
-      run: git fetch --all
+        
     - name: List current state
       run: | 
         ls

From 41ed433843de2804a393beda595bfdd7ae8d0b28 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 16:25:04 +0200
Subject: [PATCH 38/49] fix(?): path for cache

---
 .github/workflows/code_check.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 082be82..2851719 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -35,14 +35,14 @@ jobs:
       id: cache-singularity
       uses: actions/cache@v3
       with:
-        path: ~/${{ env.sif_file }}
+        path: ${{ env.sif_file }}
         key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
     - name: Pull Singularity container
       if: steps.cache-singularity.outputs.cache-hit != 'true'
       run: |
         singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
         singularity pull ${{ env.sif_file }} ${{ env.singularity_image }}
-        
+
     - name: List current state
       run: | 
         ls

From 4278a6afbd75d6484cb41298db0ffa4ebb1049a5 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 16:27:18 +0200
Subject: [PATCH 39/49] fix: step order/cache order in config_scan

---
 .github/workflows/config_scan.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 45afddc..9bc2faa 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -9,6 +9,7 @@ jobs:
   scan:
     runs-on: ubuntu-latest
     steps:
+    - uses: actions/checkout@v4
     - name: Setup Apptainer
       uses: eWaterCycle/setup-apptainer@v2
       with:
@@ -17,7 +18,7 @@ jobs:
       id: cache-singularity
       uses: actions/cache@v3
       with:
-        path: ~/${{ env.sif_file }}
+        path: ${{ env.sif_file }}
         key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
     - name: Pull Singularity container
       if: steps.cache-singularity.outputs.cache-hit != 'true'
@@ -25,7 +26,6 @@ jobs:
         singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
         singularity pull ${{ env.sif_file }} ${{ env.singularity_image }}
 
-    - uses: actions/checkout@v4
     - name: Scan classification config
       run: |
         cp -r resources/config_templates/* config/

From c2fd3cb8d12e4159fd2eec798017466e123b2fe1 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 16:27:54 +0200
Subject: [PATCH 40/49] fix: enable pylint instead of listing again

---
 .github/workflows/code_check.yml | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 2851719..9b66005 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -23,10 +23,6 @@ jobs:
     - name: Fetch all branches
       run: git fetch --all
 
-    - name: List current state
-      run: | 
-        ls
-        pwd
     - name: Setup Apptainer
       uses: eWaterCycle/setup-apptainer@v2
       with:
@@ -43,11 +39,7 @@ jobs:
         singularity registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
         singularity pull ${{ env.sif_file }} ${{ env.singularity_image }}
 
-    - name: List current state
-      run: | 
-        ls
-        pwd
-    # - name: Run Pylint
-    #   run: |
-    #     singularity exec ${{ env.sif_file }} \
-    #     pylint $(git diff --name-only origin/master...HEAD -- '*.py')
+    - name: Run Pylint
+      run: |
+        singularity exec ${{ env.sif_file }} \
+        pylint $(git diff --name-only origin/master...HEAD -- '*.py')

From c7a8a694c848f78e9e6dabc7f2f6c269fde9eca7 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 16:40:08 +0200
Subject: [PATCH 41/49] fix: add pylintrc adding the repository to python path

---
 .pylintrc | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 .pylintrc

diff --git a/.pylintrc b/.pylintrc
new file mode 100644
index 0000000..8f1de74
--- /dev/null
+++ b/.pylintrc
@@ -0,0 +1,2 @@
+[MASTER]
+init-hook='import sys; sys.path.append(".")'
\ No newline at end of file

From 00b55868f3b8a553b897318ee9285ae49f95802a Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 16:42:55 +0200
Subject: [PATCH 42/49] feat: restore code check only if py files changed

---
 .github/workflows/code_check.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 9b66005..ec5f79d 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -2,8 +2,8 @@ name: Code Checking
 
 on: 
   push:
-    # paths:
-    #   - '**/*.py'
+    paths:
+      - '**/*.py'
   pull_request:
     branches:
       - main

From f06ecc5f4caee2473c3650d159580c79a190e31c Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 16:57:47 +0200
Subject: [PATCH 43/49] fix: make code check run on pull requests to master

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

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index ec5f79d..69fc6cd 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -6,7 +6,7 @@ on:
       - '**/*.py'
   pull_request:
     branches:
-      - main
+      - master
 
 env:
   singularity_image: oras://ghcr.io/berenslab/retinal-rl:singularity-image-latest

From 7770a4b3c43369bb2fe137480076386f56cf851e Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Thu, 10 Oct 2024 17:04:25 +0200
Subject: [PATCH 44/49] fix: make cache hit branch independent

---
 .github/workflows/code_check.yml  | 2 ++
 .github/workflows/config_scan.yml | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 69fc6cd..6716b2c 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -33,6 +33,8 @@ jobs:
       with:
         path: ${{ env.sif_file }}
         key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
+        restore-keys: |
+          ${{ runner.os }}-singularity-
     - name: Pull Singularity container
       if: steps.cache-singularity.outputs.cache-hit != 'true'
       run: |
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 9bc2faa..8f6051b 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -20,6 +20,8 @@ jobs:
       with:
         path: ${{ env.sif_file }}
         key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
+        restore-keys: |
+          ${{ runner.os }}-singularity-
     - name: Pull Singularity container
       if: steps.cache-singularity.outputs.cache-hit != 'true'
       run: |

From 6fbface71d4d93a38be8669fadb3ab14aaa84060 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Fri, 11 Oct 2024 10:02:16 +0200
Subject: [PATCH 45/49] revert: cross-branch caching only possible in child
 branches

---
 .github/workflows/code_check.yml  | 2 --
 .github/workflows/config_scan.yml | 2 --
 2 files changed, 4 deletions(-)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 6716b2c..69fc6cd 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -33,8 +33,6 @@ jobs:
       with:
         path: ${{ env.sif_file }}
         key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
-        restore-keys: |
-          ${{ runner.os }}-singularity-
     - name: Pull Singularity container
       if: steps.cache-singularity.outputs.cache-hit != 'true'
       run: |
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 8f6051b..9bc2faa 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -20,8 +20,6 @@ jobs:
       with:
         path: ${{ env.sif_file }}
         key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
-        restore-keys: |
-          ${{ runner.os }}-singularity-
     - name: Pull Singularity container
       if: steps.cache-singularity.outputs.cache-hit != 'true'
       run: |

From 426d0d12e2ce5bb4a5e842bf47f922ef62e5e4b6 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Fri, 11 Oct 2024 10:11:11 +0200
Subject: [PATCH 46/49] fix: doom_creator/templates.py linting errors

---
 doom_creator/util/templates.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/doom_creator/util/templates.py b/doom_creator/util/templates.py
index f093ebf..cbd8746 100644
--- a/doom_creator/util/templates.py
+++ b/doom_creator/util/templates.py
@@ -1 +1,8 @@
+"""Templates for doom scenario creation
+
+This module provides the templates for acs scripts, decorate
+definitions and the overall config (vizdoom)
+"""
 from doom_creator.util._templates import acs, decorate, vizdoom
+
+__all__ = ['acs', 'decorate', 'vizdoom']

From 3b7d091a9413575b97c1bddb44972be8542f9685 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Fri, 11 Oct 2024 10:24:39 +0200
Subject: [PATCH 47/49] fix: restore keys in action needed for cross branch
 access?

---
 .github/workflows/code_check.yml  | 3 +++
 .github/workflows/config_scan.yml | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/.github/workflows/code_check.yml b/.github/workflows/code_check.yml
index 69fc6cd..dcd5852 100644
--- a/.github/workflows/code_check.yml
+++ b/.github/workflows/code_check.yml
@@ -33,6 +33,9 @@ jobs:
       with:
         path: ${{ env.sif_file }}
         key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
+        restore-keys: |
+          ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
+          ${{ runner.os }}-singularity-
     - name: Pull Singularity container
       if: steps.cache-singularity.outputs.cache-hit != 'true'
       run: |
diff --git a/.github/workflows/config_scan.yml b/.github/workflows/config_scan.yml
index 9bc2faa..929ebb6 100644
--- a/.github/workflows/config_scan.yml
+++ b/.github/workflows/config_scan.yml
@@ -20,6 +20,9 @@ jobs:
       with:
         path: ${{ env.sif_file }}
         key: ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
+        restore-keys: |
+          ${{ runner.os }}-singularity-${{ hashFiles('~/resources/retinal-rl.def') }}
+          ${{ runner.os }}-singularity-
     - name: Pull Singularity container
       if: steps.cache-singularity.outputs.cache-hit != 'true'
       run: |

From b7c698c3da1527cf87015093a36fddb773201df3 Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Fri, 11 Oct 2024 10:29:47 +0200
Subject: [PATCH 48/49] fix: pylint suggestions for vizdoom template

---
 doom_creator/util/_templates/vizdoom.py | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/doom_creator/util/_templates/vizdoom.py b/doom_creator/util/_templates/vizdoom.py
index 52a05ea..eb03d17 100644
--- a/doom_creator/util/_templates/vizdoom.py
+++ b/doom_creator/util/_templates/vizdoom.py
@@ -1,5 +1,13 @@
-def config(scenario_name):
-    return """\
+"""
+This module contains a dummy for a vizdoom config.
+"""
+
+
+def config(scenario_name: str):
+    """Returns a config for a vizdoom game,
+    referencing {scenario_name}.zip as the scenario."""
+
+    return f"""\
 doom_scenario_path = {scenario_name}.zip
 
 living_reward = 0.0
@@ -32,6 +40,4 @@ def config(scenario_name):
 available_game_variables = {{ HEALTH }}
 
 mode = PLAYER
-""".format(
-        scenario_name=scenario_name
-    )
+"""

From 5f8ac4353c74692aef9c6c0fc2d5ba28a6b5848d Mon Sep 17 00:00:00 2001
From: Fabio Seel <fabio.seel@uni-tuebingen.de>
Date: Fri, 11 Oct 2024 11:21:36 +0200
Subject: [PATCH 49/49] feat: make build singularity container run on pull
 requests where def file changed

---
 .github/workflows/container_build.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/container_build.yml b/.github/workflows/container_build.yml
index 07760db..b047ef2 100644
--- a/.github/workflows/container_build.yml
+++ b/.github/workflows/container_build.yml
@@ -6,6 +6,11 @@ on:
   push:
     paths:
       - 'resources/retinal-rl.def'
+  pull_request:
+    branches:
+      - master
+    paths:
+      - 'resources/retinal-rl.def'
 
 jobs:
   singularity-build: