diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8687bb0..1e99a47 100644 --- a/.pre-commit-config.yaml +++ b/.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 diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 55ce1ce..87c10bc 100644 --- a/.readthedocs.yaml +++ b/.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: diff --git a/Makefile b/Makefile index d8cffdf..ef48220 100644 --- a/Makefile +++ b/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: diff --git a/pyproject.toml b/pyproject.toml index a4e1368..a0b2488 100644 --- a/pyproject.toml +++ b/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] diff --git a/src/miv_simulator/clamps/network.py b/src/miv_simulator/clamps/network.py index 1273957..c3b3535 100644 --- a/src/miv_simulator/clamps/network.py +++ b/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 diff --git a/src/miv_simulator/connections.py b/src/miv_simulator/connections.py index ff5dd6a..3eb0236 100644 --- a/src/miv_simulator/connections.py +++ b/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, diff --git a/src/miv_simulator/network.py b/src/miv_simulator/network.py index 85cab1f..ca52565 100644 --- a/src/miv_simulator/network.py +++ b/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): diff --git a/src/miv_simulator/plotting.py b/src/miv_simulator/plotting.py index b5a3b66..2c451a6 100644 --- a/src/miv_simulator/plotting.py +++ b/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 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