Cleanup dependency list

- Add concurrency to workflows
- Fixup mypy config
- Update uv lockfile

Author: larsevj

.github/workflows/docs.yml

@@ -4,6 +4,10 @@ permissions:
 
 on: [pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
   UV_FROZEN: true # https://docs.astral.sh/uv/configuration/environment/#uv_frozen
 

.github/workflows/precommit.yml

@@ -4,6 +4,10 @@ permissions:
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
   UV_FROZEN: true # https://docs.astral.sh/uv/configuration/environment/#uv_frozen
 

.github/workflows/testing.yml

@@ -4,6 +4,10 @@ permissions:
 
 on: [pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
   UV_FROZEN: true # https://docs.astral.sh/uv/configuration/environment/#uv_frozen
 

.mypy.ini

@@ -1,9 +1 @@
 [mypy]
-
-[mypy-iterative_ensemble_smoother._ies.*]
-ignore_missing_imports = True
-ignore_errors = True
-
-[mypy-iterative_ensemble_smoother/experimental.*]
-ignore_missing_imports = True
-ignore_errors = True

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.12"
 
 python:
   install:

pyproject.toml

@@ -15,7 +15,13 @@ classifiers=[
     "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: 3.14",
 ]
-dependencies = ["numpy", "scipy", "joblib", "networkx", "scikit-learn"]
+dependencies = [
+    "joblib",
+    "networkx",
+    "numpy",
+    "scikit-learn",
+    "scipy",
+]
 dynamic=["version"] # setuptools_scm extracts Python package versions from git
 
 authors = [
@@ -37,6 +43,16 @@ text = "GPL-3.0"
 "Documentation" = "https://iterative_ensemble_smoother.readthedocs.io/en/stable/"
 
 [project.optional-dependencies]
+dev = [
+    "pytest",
+    "pytest-snapshot",
+    "pytest-memray",
+    "pre-commit",
+    "matplotlib",
+    "mypy",
+    "pandas",
+    "p_tqdm",
+]
 doc = [
     "sphinx",
     "setuptools",
@@ -53,25 +69,10 @@ doc = [
     "ipykernel",
     "ipywidgets",
     "numpydoc",
-    "scipy",
     "jinja2",
     "myst_nb",
     "lxml_html_clean"
 ]
-dev = [
-    "pytest",
-    "pytest-snapshot",
-    "pytest-memray",
-    "tox",
-    "pre-commit",
-    "matplotlib",
-    "scipy",
-    "mypy",
-    "pandas",
-    "p_tqdm",
-    "pylint",
-    "gaussianfft"
-]
 # 'scikit-sparse' version and SuiteSparse must match (depends on Ubuntu)
 sparse = ["scikit-sparse==0.4.16"]
 # setuptools_scm also writes the version to a file so that one can use the
@@ -162,6 +163,7 @@ exclude = [
     "dist",
     "node_modules",
     "venv",
+    "src/iterative_ensemble_smoother/_version.py",
 ]
 
 # Allow unused variables when underscore-prefixed.

tests/test_esmda.py

@@ -215,7 +215,7 @@ def setup_large():
 
 
 class TestOverwriteMemory:
-    @pytest.mark.limit_memory("54 MB")
+    @pytest.mark.limit_memory("58 MB")
     def test_ESMDA_memory_usage_without_overwrite(self, setup_large):
         X_prior, Y_prior, covariance, observations = setup_large
 
@@ -224,7 +224,7 @@ def test_ESMDA_memory_usage_without_overwrite(self, setup_large):
             esmda.prepare_assimilation(Y=Y_prior, overwrite=False)
             esmda.assimilate_batch(X=X_prior, overwrite=False)
 
-    @pytest.mark.limit_memory("46 MB")
+    @pytest.mark.limit_memory("50 MB")
     def test_ESMDA_memory_usage_with_overwrite(self, setup_large):
         X_prior, Y_prior, covariance, observations = setup_large