From 28d55aaf52ca62c6d97a8b9125ad6bae9c2d3aac Mon Sep 17 00:00:00 2001
From: Ilyes Batatia <48651863+ilyes319@users.noreply.github.com>
Date: Tue, 23 Apr 2024 20:53:42 +0100
Subject: [PATCH 1/9] add pylint to pre-commit

---
 .pre-commit-config.yaml     | 71 ++++++++++++++++++++-----------------
 mace/cli/run_train.py       |  2 +-
 mace/tools/scripts_utils.py |  4 +--
 3 files changed, 41 insertions(+), 36 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 32319396..ae573d90 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,9 +1,17 @@
+exclude: &exclude_files >
+    (?x)^(
+        docs/.*|
+        tests/.*|
+        .github/.*|
+        LICENSE|
+    )$
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v2.5.0
     hooks:
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
+    -   id: mixed-line-ending
+    -   id: trailing-whitespace
 
   - repo: https://github.com/psf/black-pre-commit-mirror
     rev: 23.12.1
@@ -17,34 +25,31 @@ repos:
       - id: isort
         name: Sort imports
 
-  # Failing - to be investigated separately
-  # - repo: local
-  #   hooks:
-  #     - id: pylint
-  #       name: Pylint Checks
-  #       entry: pylint
-  #       language: system
-  #       types: [python]
-  #       args:
-  #         [
-  #           "--rcfile=pyproject.toml", 
-  #           "mace", 
-  #           "tests", 
-  #           "scripts"
-  #         ]  
-  
-  # - repo: local
-  #   hooks:
-  #     - id: mypy
-  #       name: mypy type checks
-  #       entry: mypy
-  #       language: system
-  #       types: [python]
-  #       args:
-  #         [
-  #           --config-file=.mypy.ini,
-  #           mace,
-  #           tests,
-  #           scripts
-  #         ]
+  - repo: https://github.com/PyCQA/pylint
+    rev: pylint-2.5.2
+    hooks:
+    -   id: pylint
+        language: system
+        args: [
+          '--disable=line-too-long',
+          '--disable=no-member',
+          '--disable=missing-module-docstring',
+          '--disable=missing-class-docstring',
+          '--disable=missing-function-docstring',
+          '--disable=too-many-arguments',
+          '--disable=too-many-locals',
+          '--disable=not-callable',
+          '--disable=logging-fstring-interpolation',
+          '--disable=logging-not-lazy',
+          '--disable=invalid-name',
+          '--disable=too-few-public-methods',
+          '--disable=too-many-instance-attributes',
+          '--disable=too-many-statements',
+          '--disable=too-many-branches',
+          '--disable=import-outside-toplevel',
+          '--disable=cell-var-from-loop',
+          '--disable=duplicate-code',
+        ]
+        exclude: *exclude_files
+
   
\ No newline at end of file
diff --git a/mace/cli/run_train.py b/mace/cli/run_train.py
index 050e896a..d1957dea 100644
--- a/mace/cli/run_train.py
+++ b/mace/cli/run_train.py
@@ -823,7 +823,7 @@ def main() -> None:
                         path_complied,
                         _extra_files=extra_files,
                     )
-                except Exception as e:  # pylint: disable=W070344
+                except Exception as e:  # pylint: disable=W0703
                     pass
 
         if args.distributed:
diff --git a/mace/tools/scripts_utils.py b/mace/tools/scripts_utils.py
index 756627ad..17630bf3 100644
--- a/mace/tools/scripts_utils.py
+++ b/mace/tools/scripts_utils.py
@@ -388,9 +388,9 @@ def step(self, metrics=None, epoch=None):  # pylint: disable=E1123
         if self.scheduler == "ExponentialLR":
             self.lr_scheduler.step(epoch=epoch)
         elif self.scheduler == "ReduceLROnPlateau":
-            self.lr_scheduler.step(
+            self.lr_scheduler.step(  # pylint: disable=E1123
                 metrics=metrics, epoch=epoch
-            )  # pylint: disable=E1123
+            )
 
     def __getattr__(self, name):
         if name == "step":

From 4b1fc6950eb6edba9e25e17d89ae3f1f9f0ad05b Mon Sep 17 00:00:00 2001
From: Ilyes Batatia <48651863+ilyes319@users.noreply.github.com>
Date: Tue, 23 Apr 2024 21:07:23 +0100
Subject: [PATCH 2/9] format with black

---
 .github/workflows/pre-commit.yaml | 13 +++++++
 mace/cli/active_learning_md.py    |  1 +
 mace/data/utils.py                |  6 ++--
 mace/tools/finetuning_utils.py    | 58 +++++++++++++++----------------
 4 files changed, 46 insertions(+), 32 deletions(-)

diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml
index 6cfe0e02..74b8bf13 100644
--- a/.github/workflows/pre-commit.yaml
+++ b/.github/workflows/pre-commit.yaml
@@ -11,4 +11,17 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+          cache: "pip"
+
+      - name: Install requirements
+        run: |
+          pip install -U pip
+          pip install pylint
+
+      - name: Log installed environment
+        run: |
+          python3 -m pip freeze
+
       - uses: pre-commit/action@v3.0.0
diff --git a/mace/cli/active_learning_md.py b/mace/cli/active_learning_md.py
index cd5c8cb0..de4bbc1d 100644
--- a/mace/cli/active_learning_md.py
+++ b/mace/cli/active_learning_md.py
@@ -1,4 +1,5 @@
 """Demonstrates active learning molecular dynamics with constant temperature."""
+
 import argparse
 import os
 import time
diff --git a/mace/data/utils.py b/mace/data/utils.py
index a6153665..ba76423e 100644
--- a/mace/data/utils.py
+++ b/mace/data/utils.py
@@ -246,9 +246,9 @@ def load_from_xyz(
                 isolated_atom_config = atoms.info.get("config_type") == "IsolatedAtom"
                 if isolated_atom_config:
                     if energy_key in atoms.info.keys():
-                        atomic_energies_dict[
-                            atoms.get_atomic_numbers()[0]
-                        ] = atoms.info[energy_key]
+                        atomic_energies_dict[atoms.get_atomic_numbers()[0]] = (
+                            atoms.info[energy_key]
+                        )
                     else:
                         logging.warning(
                             f"Configuration '{idx}' is marked as 'IsolatedAtom' "
diff --git a/mace/tools/finetuning_utils.py b/mace/tools/finetuning_utils.py
index 97cae96a..0aad091b 100644
--- a/mace/tools/finetuning_utils.py
+++ b/mace/tools/finetuning_utils.py
@@ -50,24 +50,24 @@ def load_foundations(
         for j in range(4):  # Assuming 4 layers in conv_tp_weights,
             layer_name = f"layer{j}"
             if j == 0:
-                getattr(
-                    model.interactions[i].conv_tp_weights, layer_name
-                ).weight = torch.nn.Parameter(
-                    getattr(
-                        model_foundations.interactions[i].conv_tp_weights,
-                        layer_name,
+                getattr(model.interactions[i].conv_tp_weights, layer_name).weight = (
+                    torch.nn.Parameter(
+                        getattr(
+                            model_foundations.interactions[i].conv_tp_weights,
+                            layer_name,
+                        )
+                        .weight[:num_radial, :]
+                        .clone()
                     )
-                    .weight[:num_radial, :]
-                    .clone()
                 )
             else:
-                getattr(
-                    model.interactions[i].conv_tp_weights, layer_name
-                ).weight = torch.nn.Parameter(
-                    getattr(
-                        model_foundations.interactions[i].conv_tp_weights,
-                        layer_name,
-                    ).weight.clone()
+                getattr(model.interactions[i].conv_tp_weights, layer_name).weight = (
+                    torch.nn.Parameter(
+                        getattr(
+                            model_foundations.interactions[i].conv_tp_weights,
+                            layer_name,
+                        ).weight.clone()
+                    )
                 )
 
         model.interactions[i].linear.weight = torch.nn.Parameter(
@@ -105,24 +105,24 @@ def load_foundations(
     for i in range(2):  # Assuming 2 products modules
         max_range = max_L + 1 if i == 0 else 1
         for j in range(max_range):  # Assuming 3 contractions in symmetric_contractions
-            model.products[i].symmetric_contractions.contractions[
-                j
-            ].weights_max = torch.nn.Parameter(
-                model_foundations.products[i]
-                .symmetric_contractions.contractions[j]
-                .weights_max[indices_weights, :, :]
-                .clone()
-            )
-
-            for k in range(2):  # Assuming 2 weights in each contraction
-                model.products[i].symmetric_contractions.contractions[j].weights[
-                    k
-                ] = torch.nn.Parameter(
+            model.products[i].symmetric_contractions.contractions[j].weights_max = (
+                torch.nn.Parameter(
                     model_foundations.products[i]
                     .symmetric_contractions.contractions[j]
-                    .weights[k][indices_weights, :, :]
+                    .weights_max[indices_weights, :, :]
                     .clone()
                 )
+            )
+
+            for k in range(2):  # Assuming 2 weights in each contraction
+                model.products[i].symmetric_contractions.contractions[j].weights[k] = (
+                    torch.nn.Parameter(
+                        model_foundations.products[i]
+                        .symmetric_contractions.contractions[j]
+                        .weights[k][indices_weights, :, :]
+                        .clone()
+                    )
+                )
 
         model.products[i].linear.weight = torch.nn.Parameter(
             model_foundations.products[i].linear.weight.clone()

From 3ad2021102b0a04c1498d7936e1330a44e5977f0 Mon Sep 17 00:00:00 2001
From: Ilyes Batatia <48651863+ilyes319@users.noreply.github.com>
Date: Tue, 23 Apr 2024 21:19:31 +0100
Subject: [PATCH 3/9] exclude files in pre commit

---
 .github/workflows/pre-commit.yaml | 1 +
 .pre-commit-config.yaml           | 8 +++++---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml
index 74b8bf13..9267ce44 100644
--- a/.github/workflows/pre-commit.yaml
+++ b/.github/workflows/pre-commit.yaml
@@ -19,6 +19,7 @@ jobs:
         run: |
           pip install -U pip
           pip install pylint
+          pip install -U black
 
       - name: Log installed environment
         run: |
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ae573d90..8ac8fa5a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,6 +4,7 @@ exclude: &exclude_files >
         tests/.*|
         .github/.*|
         LICENSE|
+        README|
     )$
 
 repos:
@@ -12,18 +13,21 @@ repos:
     hooks:
     -   id: mixed-line-ending
     -   id: trailing-whitespace
+        exclude: *exclude_files
 
   - repo: https://github.com/psf/black-pre-commit-mirror
     rev: 23.12.1
     hooks:
       - id: black
         name: Black Formating
+        exclude: *exclude_files
 
   - repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:
       - id: isort
         name: Sort imports
+        exclude: *exclude_files
 
   - repo: https://github.com/PyCQA/pylint
     rev: pylint-2.5.2
@@ -50,6 +54,4 @@ repos:
           '--disable=cell-var-from-loop',
           '--disable=duplicate-code',
         ]
-        exclude: *exclude_files
-
-  
\ No newline at end of file
+        exclude: *exclude_files
\ No newline at end of file

From 4b3f1471acd212af2cf9a08a16d5df23389a0704 Mon Sep 17 00:00:00 2001
From: Ilyes Batatia <48651863+ilyes319@users.noreply.github.com>
Date: Tue, 23 Apr 2024 21:23:50 +0100
Subject: [PATCH 4/9] add run black to pre commit

---
 .github/workflows/pre-commit.yaml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml
index 9267ce44..a9e2859a 100644
--- a/.github/workflows/pre-commit.yaml
+++ b/.github/workflows/pre-commit.yaml
@@ -10,19 +10,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: "3.10"
           cache: "pip"
-
       - name: Install requirements
         run: |
           pip install -U pip
           pip install pylint
           pip install -U black
-
-      - name: Log installed environment
+      - name: Run black
         run: |
-          python3 -m pip freeze
-
+          python -m black .
       - uses: pre-commit/action@v3.0.0

From c6a302b7f788860b07a967f579903da0afdd871f Mon Sep 17 00:00:00 2001
From: Ilyes Batatia <48651863+ilyes319@users.noreply.github.com>
Date: Tue, 23 Apr 2024 21:26:28 +0100
Subject: [PATCH 5/9] update black rev in pre commit

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8ac8fa5a..bbaa104a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -16,7 +16,7 @@ repos:
         exclude: *exclude_files
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.12.1
+    rev: 24.4.0
     hooks:
       - id: black
         name: Black Formating

From c097eb34b7a6d66f51a111eb2f75753b3a0b1ae3 Mon Sep 17 00:00:00 2001
From: Ilyes Batatia <48651863+ilyes319@users.noreply.github.com>
Date: Tue, 23 Apr 2024 21:44:47 +0100
Subject: [PATCH 6/9] install dep for pylint

---
 .github/workflows/pre-commit.yaml | 1 +
 .pre-commit-config.yaml           | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml
index a9e2859a..6e0b07bc 100644
--- a/.github/workflows/pre-commit.yaml
+++ b/.github/workflows/pre-commit.yaml
@@ -19,6 +19,7 @@ jobs:
           pip install -U pip
           pip install pylint
           pip install -U black
+          pip install .[dev]
       - name: Run black
         run: |
           python -m black .
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index bbaa104a..8d1b8ef3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -30,7 +30,7 @@ repos:
         exclude: *exclude_files
 
   - repo: https://github.com/PyCQA/pylint
-    rev: pylint-2.5.2
+    rev: pylint-2.14.1
     hooks:
     -   id: pylint
         language: system

From ed2d719b1115d257b80934777dd0f3de9446272f Mon Sep 17 00:00:00 2001
From: Ilyes Batatia <48651863+ilyes319@users.noreply.github.com>
Date: Tue, 23 Apr 2024 21:48:17 +0100
Subject: [PATCH 7/9] remove lint.yml

---
 .github/workflows/lint.yml | 46 --------------------------------------
 .pre-commit-config.yaml    |  2 +-
 2 files changed, 1 insertion(+), 47 deletions(-)
 delete mode 100644 .github/workflows/lint.yml

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
deleted file mode 100644
index 998ae250..00000000
--- a/.github/workflows/lint.yml
+++ /dev/null
@@ -1,46 +0,0 @@
-name: Linting and code formatting
-
-on: []
-  # Trigger the workflow on push or pull request,
-  # but only for the main branch
-  # push:
-  #   branches: []
-  # pull_request:
-  #   branches: []
-
-
-jobs:
-  build-linux:
-    runs-on: ubuntu-latest
-
-    steps:
-      # Setup
-      - name: Checkout
-        uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8.10
-      - name: Get cache
-        uses: actions/cache@v2
-        with:
-          path: /opt/hostedtoolcache/Python/3.8.10/x64/lib/python3.8/site-packages
-          # Look to see if there is a cache hit for the corresponding requirements file
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
-
-      # Install packages
-      - name: Install packages required for installation
-        run: python -m pip install --upgrade pip setuptools wheel
-      - name: Install dependencies
-        run: pip install -r requirements.txt
-
-      # Check code
-      - name: Check formatting with yapf
-        run: python -m yapf --style=.style.yapf --diff --recursive .
-#      - name: Lint with flake8
-#        run: flake8 --config=.flake8 .
-#      - name: Check type annotations with mypy
-#        run: mypy --config-file=.mypy.ini .
-
-      - name: Test with pytest
-        run: python -m pytest tests
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8d1b8ef3..bbaa104a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -30,7 +30,7 @@ repos:
         exclude: *exclude_files
 
   - repo: https://github.com/PyCQA/pylint
-    rev: pylint-2.14.1
+    rev: pylint-2.5.2
     hooks:
     -   id: pylint
         language: system

From b553dce756648360f000f88927c2e86d1ae4bdfc Mon Sep 17 00:00:00 2001
From: Ilyes Batatia <48651863+ilyes319@users.noreply.github.com>
Date: Tue, 23 Apr 2024 22:08:40 +0100
Subject: [PATCH 8/9] fix pylint for precommit

---
 .github/workflows/pre-commit.yaml | 2 ++
 .pre-commit-config.yaml           | 1 +
 mace/cli/preprocess_data.py       | 3 +--
 pyproject.toml                    | 1 +
 setup.cfg                         | 1 +
 5 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml
index 6e0b07bc..aaf7f8b6 100644
--- a/.github/workflows/pre-commit.yaml
+++ b/.github/workflows/pre-commit.yaml
@@ -20,6 +20,8 @@ jobs:
           pip install pylint
           pip install -U black
           pip install .[dev]
+          pip install wandb
+          pip install tqdm
       - name: Run black
         run: |
           python -m black .
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index bbaa104a..e2634588 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -53,5 +53,6 @@ repos:
           '--disable=import-outside-toplevel',
           '--disable=cell-var-from-loop',
           '--disable=duplicate-code',
+          '--disable=use-dict-literal',
         ]
         exclude: *exclude_files
\ No newline at end of file
diff --git a/mace/cli/preprocess_data.py b/mace/cli/preprocess_data.py
index 23dfd3f2..988cc3cc 100644
--- a/mace/cli/preprocess_data.py
+++ b/mace/cli/preprocess_data.py
@@ -78,8 +78,7 @@ def split_array(a: np.ndarray, max_size: int):
         for j in range(0, len(factors) - i + 1):
             if np.prod(factors[j : j + i]) <= max_size:
                 test = np.prod(factors[j : j + i])
-                if test > max_factor:
-                    max_factor = test
+                max_factor = max(test, max_factor)
     return np.array_split(a, max_factor), drop_last
 
 
diff --git a/pyproject.toml b/pyproject.toml
index 8de9c0dc..05037dc7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,6 +30,7 @@ disable = [
     "import-outside-toplevel",
     "cell-var-from-loop",
     "duplicate-code",
+    "use-dict-literal",
 ]
 
 [tool.pylint.MASTER]
diff --git a/setup.cfg b/setup.cfg
index 6ed557ed..c8a246df 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -27,6 +27,7 @@ install_requires =
     python-hostlist
     configargparse
     GitPython
+    tqdm
     # for plotting:
     matplotlib
     pandas

From 6388f5d4d988d0f0111c8a463eb52d55f3564f51 Mon Sep 17 00:00:00 2001
From: Ilyes Batatia <48651863+ilyes319@users.noreply.github.com>
Date: Tue, 23 Apr 2024 22:36:14 +0100
Subject: [PATCH 9/9] ignore readme in precommit

---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e2634588..ae4223d7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,8 +3,8 @@ exclude: &exclude_files >
         docs/.*|
         tests/.*|
         .github/.*|
-        LICENSE|
-        README|
+        LICENSE.md|
+        README.md|
     )$
 
 repos: