From c0c77f338681472ba30117d648514c1e7c866f0b Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 15:20:57 +0200
Subject: [PATCH 01/20] move dssp and msms out of the yml env file

---
 .github/actions/install-python-and-package/action.yml | 9 +++++++++
 env/deeprank2.yml                                     | 2 --
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/.github/actions/install-python-and-package/action.yml b/.github/actions/install-python-and-package/action.yml
index 9f725336..1c445359 100644
--- a/.github/actions/install-python-and-package/action.yml
+++ b/.github/actions/install-python-and-package/action.yml
@@ -51,6 +51,15 @@ runs:
         which python3
         python3 --version
 
+    - name: Install dependencies
+      shell: bash -l {0}
+      run: |
+        # Install deeprank2 conda dependencies
+        ## DSSP
+        conda install -c sbl dssp>=4.2.2.1
+        ## MSMS
+        conda install -c bioconda msms>=2.6.1
+
     - name: Install the GitHub repository version of the package
       shell: bash -l {0}
       if: ${{ inputs.pkg-installation-type == 'repository' }}
diff --git a/env/deeprank2.yml b/env/deeprank2.yml
index e73ab82d..a60925bf 100644
--- a/env/deeprank2.yml
+++ b/env/deeprank2.yml
@@ -11,8 +11,6 @@ dependencies:
   - pip>=23.3
   - notebook>=7.0.6
   - sbl::libcifpp>=5.1.0
-  - sbl::dssp>=4.2.2.1
-  - msms>=2.6.1
   - markov_clustering>=0.0.6
   - pytorch=2.1.1
   - torchvision>=0.16.1

From 0b09ad718832504fb58973a358d0c5d6c4322f10 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 16:42:39 +0200
Subject: [PATCH 02/20] move standard deps to project.toml

---
 env/deeprank2.yml | 18 ------------------
 pyproject.toml    | 20 ++++++++++++++++++++
 2 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/env/deeprank2.yml b/env/deeprank2.yml
index a60925bf..be4a6cf1 100644
--- a/env/deeprank2.yml
+++ b/env/deeprank2.yml
@@ -9,9 +9,7 @@ channels:
 dependencies:
   - python==3.10
   - pip>=23.3
-  - notebook>=7.0.6
   - sbl::libcifpp>=5.1.0
-  - markov_clustering>=0.0.6
   - pytorch=2.1.1
   - torchvision>=0.16.1
   - torchaudio>=2.1.1
@@ -21,21 +19,5 @@ dependencies:
   - pytorch-sparse>=0.6.18
   - pytorch-cluster>=1.6.3
   - pytorch-spline-conv>=1.2.2
-  - tables>=3.8.0
-  - numpy>=1.21.5
-  - scipy>=1.13.1
-  - h5py>=3.6.0
-  - networkx>=2.6.3
-  - matplotlib>=3.5.1
-  - scikit-learn>=1.0.2
-  - chart-studio>=1.1.0
   - biopython>=1.81
-  - pdb2sql>=0.5.1
-  - python-louvain>=0.16
-  - tqdm>=4.63.0
   - freesasa>=2.1.0
-  - tensorboard>=0.9.0
-  - protobuf>=3.20.1
-  - ruff>=0.3.0
-  - dill>=0.3.8
-  - pyarrow>=15.0.0
diff --git a/pyproject.toml b/pyproject.toml
index 6b79b106..a796ec9c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,6 +34,25 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.10",
 ]
+dependencies = [
+    "notebook >= 7.0.6",
+    "markov_clustering >= 0.0.6",
+    "tensorboard>=0.9.0",
+    "protobuf >= 3.20.1",
+    "dill >= 0.3.8",
+    "pyarrow >= 15.0.0",
+    "tables >= 3.8.0",
+    "numpy >= 1.21.5",
+    "scipy >= 1.13.1",
+    "h5py >= 3.6.0",
+    "networkx >= 2.6.3",
+    "matplotlib >= 3.5.1",
+    "scikit-learn >= 1.0.2",
+    "chart-studio >= 1.1.0",
+    "pdb2sql >= 0.5.1",
+    "python-louvain >= 0.16",
+    "tqdm >= 4.63.0"
+    ]
 
 [project.optional-dependencies]
 # development dependency groups
@@ -45,6 +64,7 @@ test = [
     "pytest-cov",
     "pytest-runner",
     "coveralls",
+    "ruff>=0.3.0"
 ]
 publishing = ["build", "twine", "wheel"]
 notebooks = ["nbmake"]

From 89fe334de719e1db2343e8f6b85d4101b2d11912 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 16:48:12 +0200
Subject: [PATCH 03/20] fix markov-clustering dep

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a796ec9c..81c71412 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,7 +36,7 @@ classifiers = [
 ]
 dependencies = [
     "notebook >= 7.0.6",
-    "markov_clustering >= 0.0.6",
+    "markov-clustering >= 0.0.6",
     "tensorboard>=0.9.0",
     "protobuf >= 3.20.1",
     "dill >= 0.3.8",

From 95816825c693a2f01b0d2d57c21045adc9cc2173 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 17:14:55 +0200
Subject: [PATCH 04/20] add dev0 to markov clustering

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 81c71412..20a57b5b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,7 +36,7 @@ classifiers = [
 ]
 dependencies = [
     "notebook >= 7.0.6",
-    "markov-clustering >= 0.0.6",
+    "markov-clustering >= 0.0.6.dev0",
     "tensorboard>=0.9.0",
     "protobuf >= 3.20.1",
     "dill >= 0.3.8",

From ee08b3a51160bbb0f6820867282521266b306b5e Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 17:22:00 +0200
Subject: [PATCH 05/20] fix numpy version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 20a57b5b..5ae98d07 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,7 +42,7 @@ dependencies = [
     "dill >= 0.3.8",
     "pyarrow >= 15.0.0",
     "tables >= 3.8.0",
-    "numpy >= 1.21.5",
+    "numpy >= 1.25, < 2.0",
     "scipy >= 1.13.1",
     "h5py >= 3.6.0",
     "networkx >= 2.6.3",

From 476fd654a525af4fd54cd2ccb2113225fa8da398 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 17:28:46 +0200
Subject: [PATCH 06/20] fix ruff error

---
 deeprank2/features/secondary_structure.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/deeprank2/features/secondary_structure.py b/deeprank2/features/secondary_structure.py
index a29b508c..ae080272 100644
--- a/deeprank2/features/secondary_structure.py
+++ b/deeprank2/features/secondary_structure.py
@@ -103,7 +103,7 @@ def _get_secstructure(pdb_path: str) -> dict:
 
     try:
         dssp = DSSP(model, pdb_path, dssp="mkdssp")
-    except Exception as e:  # noqa: BLE001, namely: # improperly formatted pdb files raise: `Exception: DSSP failed to produce an output`
+    except Exception as e:
         pdb_format_link = "https://www.wwpdb.org/documentation/file-format-content/format33/sect1.html#Order"
         msg = (
             f"DSSP has raised the following exception: {e}.\n\t"

From 28afabe8c70babcc1f1583be904004f7ad7ff736 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 17:30:11 +0200
Subject: [PATCH 07/20] add freesasa and biopython to pip deps

---
 pyproject.toml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5ae98d07..cc71e904 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,7 +51,9 @@ dependencies = [
     "chart-studio >= 1.1.0",
     "pdb2sql >= 0.5.1",
     "python-louvain >= 0.16",
-    "tqdm >= 4.63.0"
+    "tqdm >= 4.63.0",
+    "freesasa >= 2.1.0",
+    "biopython >= 1.81"
     ]
 
 [project.optional-dependencies]

From f1ed6482edd3110212e887041071ceb235a330e4 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 17:37:34 +0200
Subject: [PATCH 08/20] move libcifpp out of the env file

---
 .github/actions/install-python-and-package/action.yml | 4 ++--
 env/deeprank2.yml                                     | 3 ---
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/actions/install-python-and-package/action.yml b/.github/actions/install-python-and-package/action.yml
index 1c445359..194c3e51 100644
--- a/.github/actions/install-python-and-package/action.yml
+++ b/.github/actions/install-python-and-package/action.yml
@@ -55,8 +55,8 @@ runs:
       shell: bash -l {0}
       run: |
         # Install deeprank2 conda dependencies
-        ## DSSP
-        conda install -c sbl dssp>=4.2.2.1
+        ## DSSP and libcifpp
+        conda install -c sbl dssp >= 4.2.2.1 libcifpp >= 5.1.0
         ## MSMS
         conda install -c bioconda msms>=2.6.1
 
diff --git a/env/deeprank2.yml b/env/deeprank2.yml
index be4a6cf1..cb431106 100644
--- a/env/deeprank2.yml
+++ b/env/deeprank2.yml
@@ -9,7 +9,6 @@ channels:
 dependencies:
   - python==3.10
   - pip>=23.3
-  - sbl::libcifpp>=5.1.0
   - pytorch=2.1.1
   - torchvision>=0.16.1
   - torchaudio>=2.1.1
@@ -19,5 +18,3 @@ dependencies:
   - pytorch-sparse>=0.6.18
   - pytorch-cluster>=1.6.3
   - pytorch-spline-conv>=1.2.2
-  - biopython>=1.81
-  - freesasa>=2.1.0

From 84032453b025db9215ee7e7c23b4ef82edc288a1 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 17:44:49 +0200
Subject: [PATCH 09/20] add quotation marks

---
 .github/actions/install-python-and-package/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/install-python-and-package/action.yml b/.github/actions/install-python-and-package/action.yml
index 194c3e51..de5e3e45 100644
--- a/.github/actions/install-python-and-package/action.yml
+++ b/.github/actions/install-python-and-package/action.yml
@@ -56,7 +56,7 @@ runs:
       run: |
         # Install deeprank2 conda dependencies
         ## DSSP and libcifpp
-        conda install -c sbl dssp >= 4.2.2.1 libcifpp >= 5.1.0
+        conda install -c sbl 'dssp >= 4.2.2.1' 'libcifpp >= 5.1.0'
         ## MSMS
         conda install -c bioconda msms>=2.6.1
 

From 5cdb3c4cbc3aabf8d2e8d548d9e9a94509327ea9 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 17:52:28 +0200
Subject: [PATCH 10/20] move torch installation to pip

---
 env/deeprank2.yml | 4 ----
 pyproject.toml    | 5 ++++-
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/env/deeprank2.yml b/env/deeprank2.yml
index cb431106..c3e29ffd 100644
--- a/env/deeprank2.yml
+++ b/env/deeprank2.yml
@@ -9,10 +9,6 @@ channels:
 dependencies:
   - python==3.10
   - pip>=23.3
-  - pytorch=2.1.1
-  - torchvision>=0.16.1
-  - torchaudio>=2.1.1
-  - cpuonly>=2.0
   - pyg>=2.4.0
   - pytorch-scatter>=2.1.2
   - pytorch-sparse>=0.6.18
diff --git a/pyproject.toml b/pyproject.toml
index cc71e904..0338199d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,7 +53,10 @@ dependencies = [
     "python-louvain >= 0.16",
     "tqdm >= 4.63.0",
     "freesasa >= 2.1.0",
-    "biopython >= 1.81"
+    "biopython >= 1.81",
+    "torch == 2.1.1", 
+    "torchvision >= 0.16.1",
+    "torchaudio >= 2.1.1"
     ]
 
 [project.optional-dependencies]

From b0f1060354b40cab40795f9700fd8eb1d0aef933 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 18:00:21 +0200
Subject: [PATCH 11/20] set torchvision and torchaudio versions

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0338199d..60cce199 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -55,8 +55,8 @@ dependencies = [
     "freesasa >= 2.1.0",
     "biopython >= 1.81",
     "torch == 2.1.1", 
-    "torchvision >= 0.16.1",
-    "torchaudio >= 2.1.1"
+    "torchvision == 0.16.1",
+    "torchaudio == 2.1.1"
     ]
 
 [project.optional-dependencies]

From 56929ffcd9d67822c53742361a69079834591847 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 18:24:54 +0200
Subject: [PATCH 12/20] move torch back to conda

---
 .github/actions/install-python-and-package/action.yml | 6 +++++-
 env/deeprank2.yml                                     | 5 -----
 pyproject.toml                                        | 5 +----
 3 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/.github/actions/install-python-and-package/action.yml b/.github/actions/install-python-and-package/action.yml
index de5e3e45..3e59c1a4 100644
--- a/.github/actions/install-python-and-package/action.yml
+++ b/.github/actions/install-python-and-package/action.yml
@@ -56,9 +56,13 @@ runs:
       run: |
         # Install deeprank2 conda dependencies
         ## DSSP and libcifpp
-        conda install -c sbl 'dssp >= 4.2.2.1' 'libcifpp >= 5.1.0'
+        conda install -c sbl dssp>=4.2.2.1 libcifpp>=5.1.0
         ## MSMS
         conda install -c bioconda msms>=2.6.1
+        ## Pytorch
+        conda install -c pytorch pytorch=2.1.1 torchvision>=0.16.1 torchaudio>=2.1.1 cpuonly>=2.0
+        ## PyG
+        conda install -c pyg pyg>=2.4.0 pytorch-scatter>=2.1.2 pytorch-sparse>=0.6.18 pytorch-cluster>=1.6.3 pytorch-spline-conv>=1.2.2
 
     - name: Install the GitHub repository version of the package
       shell: bash -l {0}
diff --git a/env/deeprank2.yml b/env/deeprank2.yml
index c3e29ffd..292e580d 100644
--- a/env/deeprank2.yml
+++ b/env/deeprank2.yml
@@ -9,8 +9,3 @@ channels:
 dependencies:
   - python==3.10
   - pip>=23.3
-  - pyg>=2.4.0
-  - pytorch-scatter>=2.1.2
-  - pytorch-sparse>=0.6.18
-  - pytorch-cluster>=1.6.3
-  - pytorch-spline-conv>=1.2.2
diff --git a/pyproject.toml b/pyproject.toml
index 60cce199..cc71e904 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,10 +53,7 @@ dependencies = [
     "python-louvain >= 0.16",
     "tqdm >= 4.63.0",
     "freesasa >= 2.1.0",
-    "biopython >= 1.81",
-    "torch == 2.1.1", 
-    "torchvision == 0.16.1",
-    "torchaudio == 2.1.1"
+    "biopython >= 1.81"
     ]
 
 [project.optional-dependencies]

From d20efe1fea2c32ebf95b058f321e4db03b1b0949 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 18:31:42 +0200
Subject: [PATCH 13/20] remove env file

---
 env/deeprank2.yml | 11 -----------
 1 file changed, 11 deletions(-)
 delete mode 100644 env/deeprank2.yml

diff --git a/env/deeprank2.yml b/env/deeprank2.yml
deleted file mode 100644
index 292e580d..00000000
--- a/env/deeprank2.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-name: deeprank2
-channels:
-  - pytorch
-  - pyg
-  - bioconda
-  - defaults
-  - conda-forge
-  - sbl
-dependencies:
-  - python==3.10
-  - pip>=23.3

From 289719a0fd0bd3377e6f4019886c4136aadcb255 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Mon, 17 Jun 2024 18:33:59 +0200
Subject: [PATCH 14/20] remove env yml from action.yml

---
 .github/actions/install-python-and-package/action.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/actions/install-python-and-package/action.yml b/.github/actions/install-python-and-package/action.yml
index 3e59c1a4..8aaf181b 100644
--- a/.github/actions/install-python-and-package/action.yml
+++ b/.github/actions/install-python-and-package/action.yml
@@ -37,7 +37,6 @@ runs:
         channels: conda-forge
         python-version: ${{ inputs.python-version }}
         activate-environment: deeprank2
-        environment-file: env/deeprank2.yml
         use-mamba: true
 
     - run: |

From bc025d962d8c4cd1a96442cc1acb8f578ddd2e50 Mon Sep 17 00:00:00 2001
From: Dani Bodor <d.bodor@esciencecenter.nl>
Date: Tue, 18 Jun 2024 17:02:07 +0200
Subject: [PATCH 15/20] ci: simplify lint action

this action doesn't require the entire package to be built, merely ruff to be installed.
---
 .github/workflows/linting.yml | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 4f72ac07..da119dfe 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -30,7 +30,7 @@ on:
 jobs:
   build:
     if: github.event.pull_request.draft == false
-    name: Linting build
+    name: Linting
     runs-on: ${{ matrix.os }}
 
     strategy:
@@ -46,11 +46,17 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
-      - uses: ./.github/actions/install-python-and-package
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
-          extras-require: test
-      - name: Check style against standards using ruff
+      - name: Python info
+        shell: bash -l {0}
+        run: |
+          which python3
+          python3 --version
+      - name: Check linting and formatting using ruff
         run: |
-          ruff check
-          ruff format --check
+          python3 -m pip install ruff
+          ruff check || echo "Please ensure you have the latest version of ruff (`ruff -V`) installed locally." && (exit 1)
+          ruff format --check || echo "Please ensure you have the latest version of ruff (`ruff -V`) installed locally." && (exit 1)

From bd53c1f1cced96290580d6829ec96bba3e506e2f Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Thu, 20 Jun 2024 11:32:54 +0200
Subject: [PATCH 16/20] move the remaining conda deps to a yml file

---
 .../install-python-and-package/action.yml     | 13 ------------
 env/deeprank2.yml                             | 21 +++++++++++++++++++
 2 files changed, 21 insertions(+), 13 deletions(-)
 create mode 100644 env/deeprank2.yml

diff --git a/.github/actions/install-python-and-package/action.yml b/.github/actions/install-python-and-package/action.yml
index 8aaf181b..48760590 100644
--- a/.github/actions/install-python-and-package/action.yml
+++ b/.github/actions/install-python-and-package/action.yml
@@ -50,19 +50,6 @@ runs:
         which python3
         python3 --version
 
-    - name: Install dependencies
-      shell: bash -l {0}
-      run: |
-        # Install deeprank2 conda dependencies
-        ## DSSP and libcifpp
-        conda install -c sbl dssp>=4.2.2.1 libcifpp>=5.1.0
-        ## MSMS
-        conda install -c bioconda msms>=2.6.1
-        ## Pytorch
-        conda install -c pytorch pytorch=2.1.1 torchvision>=0.16.1 torchaudio>=2.1.1 cpuonly>=2.0
-        ## PyG
-        conda install -c pyg pyg>=2.4.0 pytorch-scatter>=2.1.2 pytorch-sparse>=0.6.18 pytorch-cluster>=1.6.3 pytorch-spline-conv>=1.2.2
-
     - name: Install the GitHub repository version of the package
       shell: bash -l {0}
       if: ${{ inputs.pkg-installation-type == 'repository' }}
diff --git a/env/deeprank2.yml b/env/deeprank2.yml
new file mode 100644
index 00000000..423fab5c
--- /dev/null
+++ b/env/deeprank2.yml
@@ -0,0 +1,21 @@
+name: deeprank2
+channels:
+  - pytorch
+  - pyg
+  - bioconda
+  - defaults
+  - conda-forge
+  - sbl
+dependencies:
+  - sbl::libcifpp>=5.1.0
+  - sbl::dssp>=4.2.2.1
+  - msms>=2.6.1
+  - pytorch=2.1.1
+  - torchvision>=0.16.1
+  - torchaudio>=2.1.1
+  - cpuonly>=2.0
+  - pyg>=2.4.0
+  - pytorch-scatter>=2.1.2
+  - pytorch-sparse>=0.6.18
+  - pytorch-cluster>=1.6.3
+  - pytorch-spline-conv>=1.2.2

From 90a6c0639f020c307f1abc369303a401339bdab9 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Thu, 20 Jun 2024 11:33:44 +0200
Subject: [PATCH 17/20] readd the path to the env file

---
 .github/actions/install-python-and-package/action.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/actions/install-python-and-package/action.yml b/.github/actions/install-python-and-package/action.yml
index 48760590..9f725336 100644
--- a/.github/actions/install-python-and-package/action.yml
+++ b/.github/actions/install-python-and-package/action.yml
@@ -37,6 +37,7 @@ runs:
         channels: conda-forge
         python-version: ${{ inputs.python-version }}
         activate-environment: deeprank2
+        environment-file: env/deeprank2.yml
         use-mamba: true
 
     - run: |

From f88770cd43b2e3e6499b668ba08947c8303699e5 Mon Sep 17 00:00:00 2001
From: Dani Bodor <d.bodor@esciencecenter.nl>
Date: Thu, 20 Jun 2024 13:54:22 +0200
Subject: [PATCH 18/20] ci: fix return exit code

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

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index da119dfe..4dd13612 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -58,5 +58,5 @@ jobs:
       - name: Check linting and formatting using ruff
         run: |
           python3 -m pip install ruff
-          ruff check || echo "Please ensure you have the latest version of ruff (`ruff -V`) installed locally." && (exit 1)
-          ruff format --check || echo "Please ensure you have the latest version of ruff (`ruff -V`) installed locally." && (exit 1)
+          ruff check || (echo "Please ensure you have the latest version of ruff (`ruff -V`) installed locally." && (exit 1))
+          ruff format --check || (echo "Please ensure you have the latest version of ruff (`ruff -V`) installed locally." && (exit 1))

From 0ca24d29bf1fba1ac4eae9757cab476fcfbd935e Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Thu, 20 Jun 2024 14:30:08 +0200
Subject: [PATCH 19/20] add pip installation to the docker file

---
 Dockerfile               | 2 ++
 env/deeprank2-docker.yml | 2 --
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 73be0bb8..87d47733 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -14,6 +14,8 @@ RUN \
   apt install -y gcc && \
   ## Create the environment and install the dependencies
   mamba env create -f /home/deeprank2/deeprank2-docker.yml && \
+  ## Activate the environment and install pip packages
+  /opt/conda/bin/conda run -n deeprank2 pip install -r /home/deeprank2/requirements-docker.txt && \
   ## Activate the environment automatically when entering the container
   echo "source activate deeprank2" >~/.bashrc && \
   # Get the data for running the tutorials
diff --git a/env/deeprank2-docker.yml b/env/deeprank2-docker.yml
index 3b49f806..e73ab82d 100644
--- a/env/deeprank2-docker.yml
+++ b/env/deeprank2-docker.yml
@@ -41,5 +41,3 @@ dependencies:
   - ruff>=0.3.0
   - dill>=0.3.8
   - pyarrow>=15.0.0
-  - pip:
-      - --requirement requirements-docker.txt

From 11e2594fbee561b9153899147bb9a415ff79cd60 Mon Sep 17 00:00:00 2001
From: gcroci2 <crocioni.giulia@gmail.com>
Date: Thu, 20 Jun 2024 14:48:11 +0200
Subject: [PATCH 20/20] bump2version 3.0.4

---
 .bumpversion.cfg            | 2 +-
 CITATION.cff                | 2 +-
 deeprank2/__init__.py       | 2 +-
 env/requirements-docker.txt | 2 +-
 pyproject.toml              | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 3105c38c..ea591b18 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.3
+current_version = 3.0.4
 
 [comment]
 comment = The contents of this file cannot be merged with that of setup.cfg until https://github.com/c4urself/bump2version/issues/185 is resolved
diff --git a/CITATION.cff b/CITATION.cff
index db6ac7d3..77c554f1 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -86,4 +86,4 @@ preferred-citation:
   volume: 9
 title: "DeepRank2: Mining 3D Protein Structures with Geometric Deep
   Learning"
-version: "3.0.3"
+version: "3.0.4"
diff --git a/deeprank2/__init__.py b/deeprank2/__init__.py
index 8d1c8625..8e10cb46 100644
--- a/deeprank2/__init__.py
+++ b/deeprank2/__init__.py
@@ -1 +1 @@
-__version__ = "3.0.3"
+__version__ = "3.0.4"
diff --git a/env/requirements-docker.txt b/env/requirements-docker.txt
index 538781ce..b6806165 100644
--- a/env/requirements-docker.txt
+++ b/env/requirements-docker.txt
@@ -1 +1 @@
-deeprank2==3.0.3
\ No newline at end of file
+deeprank2==3.0.4
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index cc71e904..6c95ec6c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "deeprank2"
-version = "3.0.3"
+version = "3.0.4"
 description = "DeepRank2 is an open-source deep learning framework for data mining of protein-protein interfaces or single-residue missense variants."
 readme = "README.md"
 requires-python = ">=3.10"