Merge pull request #503 from materialsproject/explicit-warning-stackl…

…evels


d80f17d unpin and update pre-commit hooks
3f607e1 add explicit stacklevel to warnings (fixes flake8 B028)
d3c690d fix dead dynamic wf doc link reported in openjournals/joss-reviews#5995 (comment)
7666ca6 add a link checker CI to catch dead doc links automatically.

.github/workflows/link-check.yml

@@ -0,0 +1,29 @@
+name: Check Links
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  check_links:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          pip install pytest-check-links nbconvert
+
+      - name: Run link check
+        run: |
+          pytest --check-links **/**/*.md **/**/*.ipynb --check-links-ignore "https://www.gauss-centre.eu"

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: "^src/atomate2/vasp/schemas/calc_types/"
 repos:
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.1.3
+    rev: v0.1.7
     hooks:
       - id: ruff
         args: [--fix]
@@ -23,18 +23,18 @@ repos:
         additional_dependencies: [black]
         exclude: ^(README.md|paper/paper.md)$
   - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+    rev: 6.1.0
     hooks:
       - id: flake8
         entry: pflake8
         files: ^src/
         additional_dependencies:
-          - pyproject-flake8==6.0.0
-          - flake8-bugbear==22.12.6
-          - flake8-typing-imports==1.14.0
-          - flake8-docstrings==1.6.0
-          - flake8-rst-docstrings==0.3.0
-          - flake8-rst==0.8.0
+          - 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 +43,7 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.6.1
+    rev: v1.7.1
     hooks:
       - id: mypy
         files: ^src/

docs/tutorials/3-defining-jobs.ipynb

@@ -103,7 +103,7 @@
    "id": "fatal-bible",
    "metadata": {},
    "source": [
-    "Jobs also have an index. This tracks the number of times the job has been \"replaced\" (replacing is covered in detail in the [Dynamic and nested Flows tutorial](dynamic-flows)).\n"
+    "Jobs also have an index. This tracks the number of times the job has been \"replaced\" (replacing is covered in detail in the [Dynamic and nested Flows tutorial](5-dynamic-flows.html)).\n"
    ]
   },
   {
@@ -233,7 +233,7 @@
    "source": [
     "from jobflow.managers.local import run_locally\n",
     "\n",
-    "response = run_locally(add(1,2))"
+    "response = run_locally(add(1, 2))"
    ]
   },
   {

paper/paper.md

@@ -206,6 +206,6 @@ Naturally, the summary presented in this article constitutes only a small subset
 
 # Acknowledgements
 
-This work was primarily funded and intellectually led by the Materials Project, which is funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, under Contract no. DE-AC02-05-CH11231: Materials Project program KC23MP. A.S.R. acknowledges support via a Miller Research Fellowship from the Miller Institute for Basic Research in Science, University of California, Berkeley. J.G would like to acknowledge the Gauss Centre for Supercomputing e.V. ([www.gauss-centre.eu](http://www.gauss-centre.eu/)) for funding workflow-related developments by providing generous computing time on the GCS Supercomputer SuperMUC-NG at Leibniz Supercomputing Centre ([www.lrz.de](http://www.lrz.de/)) (Project pn73da). J.R. acknowledges support from the German Academic Scholarship Foundation (Studienstiftung). M.L.E. thanks the BEWARE scheme of the Wallonia-Brussels Federation for funding under the European Commission's Marie Curie-Skłodowska Action (COFUND 847587). G.P. and D.W. acknowledge Umicore for the financial support in developing the remote execution mode of jobflow. D.W. and G.M.R. acknowledge funding from the European Union’s Horizon 2020 research and innovation program under the grant agreement No 951786 (NOMAD CoE). A.M.G. is supported by EPSRC Fellowship EP/T033231/1.
+This work was primarily funded and intellectually led by the Materials Project, which is funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, under Contract no. DE-AC02-05-CH11231: Materials Project program KC23MP. A.S.R. acknowledges support via a Miller Research Fellowship from the Miller Institute for Basic Research in Science, University of California, Berkeley. J.G would like to acknowledge the Gauss Centre for Supercomputing e.V. (<https://www.gauss-centre.eu>) for funding workflow-related developments by providing generous computing time on the GCS Supercomputer SuperMUC-NG at Leibniz Supercomputing Centre ([www.lrz.de](http://www.lrz.de/)) (Project pn73da). J.R. acknowledges support from the German Academic Scholarship Foundation (Studienstiftung). M.L.E. thanks the BEWARE scheme of the Wallonia-Brussels Federation for funding under the European Commission's Marie Curie-Skłodowska Action (COFUND 847587). G.P. and D.W. acknowledge Umicore for the financial support in developing the remote execution mode of jobflow. D.W. and G.M.R. acknowledge funding from the European Union’s Horizon 2020 research and innovation program under the grant agreement No 951786 (NOMAD CoE). A.M.G. is supported by EPSRC Fellowship EP/T033231/1.
 
 # References

src/jobflow/core/flow.py

@@ -274,7 +274,8 @@ def output(self, output: Any):
                     f"Flow '{self.name}' contains a Flow or Job as an output. "
                     f"Usually the Flow output should be the output of a Job or "
                     f"another Flow (e.g. job.output). If this message is "
-                    f"unexpected then double check the outputs of your Flow."
+                    f"unexpected then double check the outputs of your Flow.",
+                    stacklevel=2,
                 )
 
             # check if the jobs array contains all jobs needed for the references

src/jobflow/core/job.py

@@ -359,7 +359,8 @@ def __init__(
                 f"Job '{self.name}' contains an Flow or Job as an input. "
                 f"Usually inputs should be the output of a Job or an Flow (e.g. "
                 f"job.output). If this message is unexpected then double check the "
-                f"inputs to your Job."
+                f"inputs to your Job.",
+                stacklevel=2,
             )
 
     def __repr__(self):

src/jobflow/core/store.py

@@ -282,7 +282,7 @@ def update(
 
         from jobflow.utils.find import find_key, update_in_dictionary
 
-        if save is None or save is True:
+        if save in (None, True):
             save = self.save
 
         save_keys = _prepare_save(save)

src/jobflow/managers/local.py

@@ -156,7 +156,7 @@ def _run(root_flow):
                 response, jobflow_stopped = _run_job(job, parents)
 
             encountered_bad_response = encountered_bad_response or response is None
-            if jobflow_stopped is True:
+            if jobflow_stopped:
                 return False
 
         return not encountered_bad_response

src/jobflow/settings.py

@@ -107,7 +107,7 @@ class JobflowSettings(BaseSettings):
     JOB_STORE: JobStore = Field(
         default_factory=lambda: JobStore(
             MemoryStore(),
-            additional_stores=defaultdict(lambda: _default_additional_store()),
+            additional_stores=defaultdict(_default_additional_store),
         ),
         description="Default JobStore to use when running locally or using FireWorks. "
         "See the :obj:`JobflowSettings` docstring for more details on the "
@@ -137,7 +137,8 @@ def load_default_settings(cls, values):
         if Path(config_file_path).exists():
             if Path(config_file_path).stat().st_size == 0:
                 warnings.warn(
-                    f"An empty JobFlow config file was located at {config_file_path}"
+                    f"An empty JobFlow config file was located at {config_file_path}",
+                    stacklevel=2,
                 )
             else:
                 try:

src/jobflow/utils/enum.py

@@ -12,7 +12,7 @@ def __str__(self):
 
     def __eq__(self, other):
         """Compare to another enum for equality."""
-        if type(self) == type(other) and self.value == other.value:
+        if type(self) is type(other) and self.value == other.value:
             return True
         return str(self.value) == str(other)
 

src/jobflow/utils/find.py

@@ -233,7 +233,7 @@ def get_root_locations(locations):
         >>> _get_root_locations([["a", "b"], ["a"], ["c", "d"]])
         [["a"], ["c", "d"]]
     """
-    sorted_locs = sorted(locations, key=lambda x: len(x))
+    sorted_locs = sorted(locations, key=len)
     root_locations = []
     for loc in sorted_locs:
         if any(loc[: len(rloc)] == rloc for rloc in root_locations):

src/jobflow/utils/graph.py

@@ -46,7 +46,9 @@ def itergraph(graph: nx.DiGraph):
     subgraphs = [graph.subgraph(c) for c in nx.weakly_connected_components(graph)]
 
     if len(subgraphs) > 1:
-        warnings.warn("Some jobs are not connected, their ordering may be random")
+        warnings.warn(
+            "Some jobs are not connected, their ordering may be random", stacklevel=2
+        )
 
     for subgraph in subgraphs:
         yield from nx.topological_sort(subgraph)