Merge pull request #640 from materialsproject/uv-ci-test-lowest-highest-dep-resolution

Increase CI sensitivity by testing both lowest-direct and highest dependency resolution strategy

Author: utf

.github/workflows/testing.yml

@@ -35,14 +35,20 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10', '3.11', '3.12']
+        version:
+          - { python: "3.10", resolution: highest, extras: "tests,strict" }
+          - { python: "3.12", resolution: lowest-direct, extras: "tests" }
+          - { python: "3.12", resolution: highest, extras: tests }
+          # python 3.12 CI failing due to maggma incompatible, see
+          # https://github.com/materialsproject/jobflow/pull/640#issuecomment-2209055692
+          # - { python: "3.12", resolution: lowest-direct, extras: tests }
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.version.python }}
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -52,7 +58,7 @@ jobs:
       - name: Install dependencies
         run: |
           pip install uv
-          uv pip install .[strict,tests] --system
+          uv pip install '.[${{ matrix.version.extras }}]' --system --resolution=${{ matrix.version.resolution }}
 
       - name: Test
         run: pytest --cov=jobflow --cov-report=xml

.pre-commit-config.yaml

@@ -1,40 +1,25 @@
 default_language_version:
   python: python3
-exclude: "^src/atomate2/vasp/schemas/calc_types/"
+exclude: '^src/atomate2/vasp/schemas/calc_types/'
 repos:
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.11.12
+    rev: v0.13.0
     hooks:
       - id: ruff
         args: [--fix]
       - id: ruff-format
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
-      - id: fix-encoding-pragma
-        args: [--remove]
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.19.1
+    rev: 1.20.0
     hooks:
       - id: blacken-docs
         additional_dependencies: [black]
         exclude: ^(README.md|paper/paper.md)$
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
-    hooks:
-      - id: flake8
-        entry: pflake8
-        files: ^src/
-        additional_dependencies:
-          - pyproject-flake8
-          - flake8-bugbear
-          - flake8-typing-imports
-          - flake8-docstrings
-          - flake8-rst-docstrings
-          - flake8-rst
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
@@ -43,7 +28,7 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.0
+    rev: v1.18.1
     hooks:
       - id: mypy
         files: ^src/
@@ -58,6 +43,6 @@ repos:
         stages: [commit, commit-msg]
         args:
           - --ignore-words-list
-          - "titel,statics,ba,nd,te,atomate"
+          - 'titel,statics,ba,nd,te,atomate'
           - --check-filenames
         types_or: [python, rst, markdown]

pyproject.toml

@@ -27,13 +27,13 @@ classifiers = [
 ]
 requires-python = ">=3.10"
 dependencies = [
-    "PyYAML",
-    "maggma>=0.57.0",
+    "PyYAML>=6.0.1",
+    "maggma>=0.72.0",
     "monty>=2023.9.25",
-    "networkx",
+    "networkx>=3.2.1",
     "pydantic-settings>=2.0.3",
-    "pydantic>=2.0.1",
-    "pydash",
+    "pydantic>=2.4",
+    "pydash>=8.0.1",
 ]
 
 [project.optional-dependencies]
@@ -163,6 +163,7 @@ ignore = [
     "FBT001",
     "FBT002",
     "ISC001",
+    "PLC0415", # import should be at the top-level of a file
     "PLR0911", # too-many-return-statements
     "PLR0912", # too-many-branches
     "PLR0913", # too-many-arguments
@@ -180,5 +181,6 @@ isort.known-first-party = ["jobflow"]
 # D: pydocstyle
 # PLR2004: magic-value-comparison
 # PT004: pytest-missing-fixture-name-underscore
+
 "**/tests/*" = ["ANN", "ARG001", "D", "PLR2004", "PT004", "S101"]
 "docs/tutorials/*" = ["D", "PLR2004"]

tests/core/test_flow.py

@@ -115,12 +115,13 @@ def test_flow_of_jobs_init():
 
     # test job given rather than outputs
     add_job = get_test_job()
-    with pytest.warns(UserWarning):
+    warn_msg = "Flow 'Flow' contains a Flow or Job as an output."
+    with pytest.warns(UserWarning, match=warn_msg):
         Flow([add_job], output=add_job)
 
     # test complex object containing job given rather than outputs
     add_job = get_test_job()
-    with pytest.warns(UserWarning):
+    with pytest.warns(UserWarning, match=warn_msg):
         Flow([add_job], output={1: [[{"a": add_job}]]})
 
     # test job already belongs to another flow
@@ -203,13 +204,14 @@ def test_flow_of_flows_init():
     # test flow given rather than outputs
     add_job = get_test_job()
     sub_flow = Flow([add_job], output=add_job.output)
-    with pytest.warns(UserWarning):
+    warn_msg = "Flow 'Flow' contains a Flow or Job as an output."
+    with pytest.warns(UserWarning, match=warn_msg):
         Flow([sub_flow], output=sub_flow)
 
     # test complex object containing job given rather than outputs
     add_job = get_test_job()
     sub_flow = Flow([add_job], output=add_job.output)
-    with pytest.warns(UserWarning):
+    with pytest.warns(UserWarning, match=warn_msg):
         Flow([sub_flow], output={1: [[{"a": sub_flow}]]})
 
     # test flow already belongs to another flow
@@ -354,6 +356,8 @@ def test_graph():
 
 
 def test_draw_graph():
+    pytest.importorskip("matplotlib")
+
     from jobflow import Flow, JobOrder
 
     # test unconnected graph
@@ -383,8 +387,9 @@ def test_draw_graph():
     assert flow.draw_graph()
 
 
-@pytest.mark.usefixtures("no_pydot")
-def test_draw_graph_nopydot():
+def test_draw_graph_nopydot(no_pydot):
+    pytest.importorskip("matplotlib")
+
     from jobflow import Flow, JobOrder
 
     # test unconnected graph
@@ -714,7 +719,7 @@ def test_add_jobs():
     flow2 = Flow([flow1])
     flow3 = Flow([flow2])
     with pytest.raises(
-        ValueError, match="circular dependency: Flow .+ contains the current Flow"
+        ValueError, match=r"circular dependency: Flow .+ contains the current Flow"
     ):
         flow1.add_jobs(flow3)
 
@@ -1312,7 +1317,7 @@ def test_flow_magic_methods_edge_cases():
     ):
         _ = flow1 + job1
 
-    with pytest.raises(ValueError, match="Job .+ already belongs to another flow"):
+    with pytest.raises(ValueError, match=r"Job .+ already belongs to another flow"):
         _ = flow1 + job6
 
 

tests/core/test_job.py

@@ -33,7 +33,9 @@ def test_job_init():
     assert test_job.output.uuid == test_job.uuid
 
     # test job as another job as input
-    with pytest.warns(UserWarning):
+    with pytest.warns(
+        UserWarning, match="Job 'add' contains an Flow or Job as an input"
+    ):
         Job(function=add, function_args=(test_job,))
 
     # test init with kwargs

tests/core/test_maker.py

@@ -252,6 +252,6 @@ def bad_func(_: Maker) -> int:
     # test bad recursive call
     with pytest.raises(
         ValueError,
-        match="Function must return a Maker object. Got <class 'int'> instead.",
+        match=r"Function must return a Maker object. Got <class 'int'> instead.",
     ):
         recursive_call(maker, bad_func)

tests/core/test_store.py

@@ -32,6 +32,8 @@ def test_basic(memory_store):
 
 
 def test_additional(memory_store):
+    pytest.importorskip("moto")
+
     from copy import deepcopy
 
     import boto3

tests/managers/test_fireworks.py

@@ -1,5 +1,7 @@
 import pytest
 
+pytest.importorskip("fireworks")
+
 
 def test_flow_to_workflow(
     memory_jobstore, simple_job, simple_flow, connected_flow, nested_flow

tests/test_settings.py

@@ -79,7 +79,7 @@ def test_settings_object(clean_dir, test_data):
     with open(config_file_path, "w") as f:
         pass
 
-    with pytest.warns(UserWarning):
+    with pytest.warns(UserWarning, match="An empty JobFlow config file was located at"):
         settings = JobflowSettings()
 
     # An error should be thrown if the file exists and

tests/utils/test_graph.py

@@ -20,7 +20,7 @@ def test_itergraph():
 
     # test non-connected
     graph = DiGraph([("a", "b"), ("c", "d")])
-    with pytest.warns(UserWarning):
+    with pytest.warns(UserWarning, match="Some jobs are not connected"):
         result = list(itergraph(graph))
     assert {*result} == {"a", "b", "c", "d"}
 
@@ -33,6 +33,8 @@ def test_itergraph():
 
 
 def test_draw_graph():
+    pytest.importorskip("matplotlib")
+
     from networkx import DiGraph, planar_layout
 
     from jobflow.utils.graph import draw_graph
@@ -43,8 +45,9 @@ def test_draw_graph():
     assert draw_graph(graph, layout_function=planar_layout)
 
 
-@pytest.mark.usefixtures("no_pydot")
-def test_draw_graph_no_pydot():
+def test_draw_graph_no_pydot(no_pydot):
+    pytest.importorskip("matplotlib")
+
     from networkx import DiGraph
 
     from jobflow.utils.graph import draw_graph
@@ -53,8 +56,7 @@ def test_draw_graph_no_pydot():
     assert draw_graph(graph)
 
 
-@pytest.mark.usefixtures("no_matplotlib")
-def test_draw_graph_no_matplotlib():
+def test_draw_graph_no_matplotlib(no_matplotlib):
     from networkx import DiGraph
 
     import jobflow.utils.graph
@@ -71,6 +73,8 @@ def add(a, b):
 
 
 def test_to_pydot():
+    pytest.importorskip("pydot")
+
     from jobflow import Flow, Job
     from jobflow.utils.graph import to_pydot