Merge pull request #954 from Libensemble/formatting/all_precommit

Running all precommit hooks (except on .xml and .svg)
Libensemble · Jan 5, 2023 · 5fd6376 · 5fd6376
2 parents df7406f + cc0ed46
commit 5fd6376
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Showing 14 changed files with 40 additions and 56 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -176,7 +176,6 @@ jobs:
             sed -i -e "s/pyzmq>=22.1.0,<23.0.0/pyzmq>=23.0.0,<24.0.0/" ./balsam/setup.cfg
             cd balsam; pip install -e .; cd ..
 
-
         - name: Find MPI, Install libEnsemble, flake8, ulimit adjust
           run: |
             pip install -e .

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,8 +2,10 @@ repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.3.0
     hooks:
-    -   id: end-of-file-fixer
-    -   id: trailing-whitespace
+    - id: end-of-file-fixer
+      exclude: ^(.*\.xml|.*\.svg)$
+    - id: trailing-whitespace
+      exclude: ^(.*\.xml|.*\.svg)$
 
 - repo: https://github.com/pycqa/isort
   rev: 5.11.4
@@ -29,3 +31,4 @@ repos:
   -   id: blacken-docs
       additional_dependencies: [black==22.12.0]
       files: ^(.*\.py|.*\.rst)$
+      args: [--line-length=120]
diff --git a/docs/data_structures/data_structures.rst b/docs/data_structures/data_structures.rst
@@ -16,4 +16,4 @@ a complete libEnsemble workflow, or using the alternative yaml interface.
    alloc_specs
    persis_info
    exit_criteria
-   ensemble_specs
+   ensemble_specs
diff --git a/docs/data_structures/ensemble_specs.rst b/docs/data_structures/ensemble_specs.rst
@@ -11,4 +11,4 @@ Optional model used to validate each component of a libEnsemble workflow togethe
   :model-show-config-summary: False
   :model-show-validator-members: False
   :model-show-validator-summary: False
-  :field-list-validators: False
+  :field-list-validators: False
diff --git a/docs/dev_guide/dev_API/scheduler_module.rst b/docs/dev_guide/dev_API/scheduler_module.rst
@@ -7,4 +7,4 @@ Scheduler Module
 .. autoclass:: ResourceScheduler
   :member-order: bysource
   :members:
-  :noindex:
+  :noindex:
diff --git a/docs/examples/aposmm.rst b/docs/examples/aposmm.rst
@@ -46,4 +46,4 @@ LocalOptInterfacer
 .. _mpmath: https://pypi.org/project/mpmath
 .. _nlopt: http://ab-initio.mit.edu/wiki/index.php/NLopt
 .. _petsc4py: https://bitbucket.org/petsc/petsc4py
-.. _DFO-LS: https://github.com/numericalalgorithmsgroup/dfols
+.. _DFO-LS: https://github.com/numericalalgorithmsgroup/dfols
diff --git a/docs/examples/fd_param_finder.rst b/docs/examples/fd_param_finder.rst
@@ -2,4 +2,4 @@ persistent_fd_param_finder
 --------------------------
 .. automodule:: persistent_fd_param_finder
   :members:
-..   :undoc-members:
+..   :undoc-members:
diff --git a/docs/history_output_logging.rst b/docs/history_output_logging.rst
@@ -144,4 +144,4 @@ without simulation-specific directories.
   The ``scripts`` directory, in the libEnsemble project root directory,
   contains scripts to compare outputs and create plots based on the ensemble output.
 
-.. include:: ../scripts/readme.rst
+.. include:: ../scripts/readme.rst
diff --git a/docs/tutorials/local_sine_tutorial.rst b/docs/tutorials/local_sine_tutorial.rst
@@ -281,9 +281,7 @@ the history array. ``flag`` should be zero if no errors occur.
 .. code-block:: python
     :linenos:
 
-    H, persis_info, flag = libE(
-        sim_specs, gen_specs, exit_criteria, persis_info, libE_specs=libE_specs
-    )
+    H, persis_info, flag = libE(sim_specs, gen_specs, exit_criteria, persis_info, libE_specs=libE_specs)
 
     print([i for i in H.dtype.fields])  # (optional) to visualize our history array
     print(H)
@@ -391,9 +389,7 @@ Write a Calling Script with the following specifications:
        persis_info = add_unique_random_streams({}, nworkers + 1)
        exit_criteria = {"gen_max": 160}
 
-       H, persis_info, flag = libE(
-           sim_specs, gen_specs, exit_criteria, persis_info, libE_specs=libE_specs
-       )
+       H, persis_info, flag = libE(sim_specs, gen_specs, exit_criteria, persis_info, libE_specs=libE_specs)
 
        if flag != 0:
            print("Oh no! An error occurred!")
@@ -450,9 +446,7 @@ modify the bottom of the calling script like this:
   :linenos:
   :emphasize-lines: 4
 
-    H, persis_info, flag = libE(
-        sim_specs, gen_specs, exit_criteria, persis_info, libE_specs=libE_specs
-    )
+    H, persis_info, flag = libE(sim_specs, gen_specs, exit_criteria, persis_info, libE_specs=libE_specs)
 
     if is_manager:
         # Some (optional) statements to visualize our history array

diff --git a/examples/libE_submission_scripts/summit_submit_mproc.sh b/examples/libE_submission_scripts/summit_submit_mproc.sh
@@ -41,4 +41,4 @@ hash -r # Check no commands hashed (pip/python...)
 # Launch libE
 # python $EXE $NUM_WORKERS > out.txt 2>&1  # No args. All defined in calling script
 # python $EXE $COMMS $NWORKERS > out.txt 2>&1  # If calling script is using parse_args()
-python $EXE $LIBE_WALLCLOCK $COMMS $NWORKERS > out.txt 2>&1 # If calling script takes wall-clock as positional arg.
+python $EXE $LIBE_WALLCLOCK $COMMS $NWORKERS > out.txt 2>&1 # If calling script takes wall-clock as positional arg.
diff --git a/install/testing_requirements.txt b/install/testing_requirements.txt
@@ -5,4 +5,4 @@ pytest-cov==4.0.0
 pytest-timeout==2.1.0
 mock==4.0.3
 coveralls==3.3.1
-python-dateutil==2.8.2
+python-dateutil==2.8.2
diff --git a/libensemble/libE.py b/libensemble/libE.py
@@ -30,25 +30,19 @@
 
     libE_specs["save_every_k_gens"] = 20
 
-    gen_specs = {"gen_f": gen_random_sample,
-                 "out": [("x", float, (1,))],
-                 "user": {
-                    "lower": np.array([-3]),
-                    "upper": np.array([3]),
-                    "gen_batch_size": 5
-                    }
-                 }
+    gen_specs = {
+        "gen_f": gen_random_sample,
+        "out": [("x", float, (1,))],
+        "user": {"lower": np.array([-3]), "upper": np.array([3]), "gen_batch_size": 5},
+    }
 
-    sim_specs = {"sim_f": sim_find_sine,
-                 "in": ["x"],
-                 "out": [("y", float)]}
+    sim_specs = {"sim_f": sim_find_sine, "in": ["x"], "out": [("y", float)]}
 
-    persis_info = add_unique_random_streams({}, nworkers+1)
+    persis_info = add_unique_random_streams({}, nworkers + 1)
 
     exit_criteria = {"sim_max": 80}
 
-    H, persis_info, flag = libE(sim_specs, gen_specs, exit_criteria, persis_info,
-                                libE_specs=libE_specs)
+    H, persis_info, flag = libE(sim_specs, gen_specs, exit_criteria, persis_info, libE_specs=libE_specs)
 
 This will initiate libEnsemble with a Manager and ``nworkers`` workers (parsed from
 the command line), and runs on laptops or supercomputers. If an exception is
@@ -201,38 +195,33 @@
     from simulator import sim_find_sine
     from libensemble.tools import add_unique_random_streams
 
-    if __name__ == "__main__:
+    if __name__ == "__main__":
 
         nworkers, is_manager, libE_specs, _ = parse_args()
 
         libE_specs["save_every_k_gens"] = 20
 
-        gen_specs = {"gen_f": gen_random_sample,
-                    "out": [("x", float, (1,))],
-                    "user": {
-                        "lower": np.array([-3]),
-                        "upper": np.array([3]),
-                        "gen_batch_size": 5
-                        }
-                    }
+        gen_specs = {
+            "gen_f": gen_random_sample,
+            "out": [("x", float, (1,))],
+            "user": {"lower": np.array([-3]), "upper": np.array([3]), "gen_batch_size": 5},
+        }
 
-        sim_specs = {"sim_f": sim_find_sine,
-                    "in": ["x"],
-                    "out": [("y", float)]}
+        sim_specs = {"sim_f": sim_find_sine, "in": ["x"], "out": [("y", float)]}
 
-        persis_info = add_unique_random_streams({}, nworkers+1)
+        persis_info = add_unique_random_streams({}, nworkers + 1)
 
         exit_criteria = {"sim_max": 80}
 
-        H, persis_info, flag = libE(sim_specs, gen_specs, exit_criteria, persis_info,
-                                    libE_specs=libE_specs)
+        H, persis_info, flag = libE(sim_specs, gen_specs, exit_criteria, persis_info, libE_specs=libE_specs)
 
 Alternatively, you may set the multiprocessing start method to ``"fork"`` via the following:
 
 .. code-block:: python
     :linenos:
 
     from multiprocessing import set_start_method
+
     set_start_method("fork")
 
 But note that this is incompatible with some libraries.

diff --git a/tex/bibs/masterbib.bib b/tex/bibs/masterbib.bib
@@ -511,7 +511,7 @@ @BOOK{ATAZ89
 }
 
 @article{Gheribi20111323,
-  title = "Calculating all local minima on liquidus surfaces using the {FactSage} software and databases and the {Mesh Adaptive Direct Search} algorithm ", 
+  title = "Calculating all local minima on liquidus surfaces using the {FactSage} software and databases and the {Mesh Adaptive Direct Search} algorithm ",
   journal = "The Journal of Chemical Thermodynamics",
   volume = "43",
   number = "9",
@@ -529,7 +529,7 @@ @article{doi:10.1137/070707518
   number = {3},
   pages = {1150--1170},
   year = {2008},
-  doi = {10.1137/070707518}, 
+  doi = {10.1137/070707518},
 }
 
 @article{McKay1979,
@@ -588,7 +588,7 @@ @Misc{petsc-web-page
   uncommenthowpublished = {\url{http://www.mcs.anl.gov/petsc}},
   year = {2017}
 }
- 
+
 @Misc{nlopt,
   author = {Steven G. Johnson},
   title =  {The {NLopt} nonlinear-optimization package},

diff --git a/tex/planning_doc/Makefile b/tex/planning_doc/Makefile
@@ -3,23 +3,22 @@ TEXFILES = *.tex
 PICS = ../images
 BIBFILES = ../bibs/*.bib
 
-all: $(SOURCE).pdf 
+all: $(SOURCE).pdf
 
 $(SOURCE).pdf: $(TEXFILES) $(BIBFILES) $(PICS)
 	pdflatex $(SOURCE).tex
 	bibtex $(SOURCE)
 	pdflatex $(SOURCE).tex
 	pdflatex $(SOURCE).tex
 
-#$(preprint).pdf: $(TEXFILES) 
+#$(preprint).pdf: $(TEXFILES)
 #  pdflatex $(preprint).tex
 
-#$(response).pdf: $(TEXFILES) 
+#$(response).pdf: $(TEXFILES)
 #  pdflatex $(response).tex
 
 view: $(SOURCE).pdf
 	open $(SOURCE).pdf
 clean:
 	-rm -f  $(SOURCE).log $(SOURCE).aux $(SOURCE).bbl $(SOURCE).blg \
 	$(SOURCE).pdf $(SOURCE).out *.backup *.tex~ *.log
-