Upgrade pre-commit. Closes #81 (#86)

.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: check-json
       - id: end-of-file-fixer
-      - id: requirements-txt-fixer
-  - repo: https://github.com/psf/black
-    rev: 24.8.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.3
     hooks:
-      - id: black
-        additional_dependencies: ["click==8.0.4"]
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format

.readthedocs.yaml

@@ -7,19 +7,17 @@ submodules:
 # Set the version of Python and other tools you might need
 build:
   os: ubuntu-22.04
-  tools: {python: "3.10"}
+  tools: { python: "3.10" }
   apt_packages:
     - mpich
     - cmake
     - libhdf5-mpi-dev
   jobs:
     post_create_environment:
-      - pip install poetry
-      - poetry config virtualenvs.create false
+      - pip install uv
     post_install:
-      - pip install --upgrade pip
-      - pip install neuron
-      - poetry install --with docs
+      - uv sync --extra docs
+      - source .venv/bin/activate
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

Makefile

@@ -9,7 +9,7 @@ install:
 
 .PHONY: pre-commit-install
 pre-commit-install:
-	poetry run pre-commit install
+	uv run pre-commit install
 
 #* Formatters
 .PHONY: codestyle
@@ -23,7 +23,7 @@ formatting: codestyle
 #* Linting
 .PHONY: test
 test:
-	PYTHONPATH=$(PYTHONPATH) poetry run pytest -c pyproject.toml --cov-report=html --cov=src tests/
+	PYTHONPATH=$(PYTHONPATH) uv run pytest -c pyproject.toml --cov-report=html --cov=src tests/
 
 .PHONY: check-codestyle
 check-codestyle:

pyproject.toml

@@ -37,8 +37,9 @@ build-backend = "hatchling.build"
 
 [tool.uv]
 dev-dependencies = [
+    "pre-commit>=4.1.0",
     "pytest>=8.3.2",
-    "ruff>=0.6.9",
+    "ruff==0.9.3",
 ]
 
 [tool.uv.sources]

src/miv_simulator/clamps/network.py

@@ -147,7 +147,7 @@ def generate_weights(env, weight_source_rules, this_syn_attrs):
             else:
                 raise RuntimeError(
                     "network_clamp.generate_weights: unknown weight generator rule class "
-                    f'{weight_rule["class"]}'
+                    f"{weight_rule['class']}"
                 )
 
     return weights_dict

src/miv_simulator/connections.py

@@ -388,9 +388,9 @@ def generate_synaptic_connections(
                     f"{ranstream_syn=}"
                 )
             log_flag = False
-            assert (
-                projection is not None
-            ), f"generate_synaptic_connections: {gid=}: {syn_id=} {syn_type=} {swc_type=} {syn_layer=} {projection=} {ranstream_syn=} {population_dict=} {projection_synapse_dict=}\n {synapse_dict['syn_types']=}"
+            assert projection is not None, (
+                f"generate_synaptic_connections: {gid=}: {syn_id=} {syn_type=} {swc_type=} {syn_layer=} {projection=} {ranstream_syn=} {population_dict=} {projection_synapse_dict=}\n {synapse_dict['syn_types']=}"
+            )
             synapse_prj_counts[prj_pop_index[projection]] += 1
             synapse_prj_partition[projection][syn_layer].append(syn_id)
         it += 1
@@ -506,9 +506,9 @@ def generate_synaptic_connections(
             logger.warning(
                 f"Rank {rank}: source gid list is empty for gid: {destination_gid} source: {projection}"
             )
-        assert (
-            len(prj_source_vertices_array) > 0
-        ), f"Rank {rank}: source gid list is empty. The cell density might be too small."
+        assert len(prj_source_vertices_array) > 0, (
+            f"Rank {rank}: source gid list is empty. The cell density might be too small."
+        )
         count += len(prj_source_vertices_array)
         gid_dict[destination_gid] = (
             prj_source_vertices_array,

src/miv_simulator/network.py

@@ -63,9 +63,7 @@ def ld_bal(env):
     max_sum_cx = env.pc.allreduce(sum_cx, 2)
     sum_cx = env.pc.allreduce(sum_cx, 1)
     if rank == 0:
-        logger.info(
-            f"*** expected load balance {(((sum_cx / nhosts) / max_sum_cx)):.2f}"
-        )
+        logger.info(f"*** expected load balance {((sum_cx / nhosts) / max_sum_cx):.2f}")
 
 
 def lpt_bal(env):

src/miv_simulator/plotting.py

@@ -2298,7 +2298,7 @@ def plot_intracellular_state(
                             )
                         else:
                             legend_labels.append(
-                                f"{pop_name} {gid} " f"{cell_state_mat[2][i]}"
+                                f"{pop_name} {gid} {cell_state_mat[2][i]}"
                             )
 
                 if lowpass_plot is not None and not distance:

src/miv_simulator/simulator/generate_network_architecture.py

@@ -124,7 +124,7 @@ def rho(x):
                 )
             elif len(valid_idxs) != len(in_nodes):
                 logger.info(
-                    f"Removing {len(in_nodes)-len(valid_idxs)} out of {len(in_nodes)} nodes due to constraint {constraint}"
+                    f"Removing {len(in_nodes) - len(valid_idxs)} out of {len(in_nodes)} nodes due to constraint {constraint}"
                 )
             in_nodes = in_nodes[valid_idxs]
         node_count = len(in_nodes)