Add Pylint (#55)

* Disable PSM3 in CI pipelines

* Fix filepaths and variable names

* Python best coding practices

Address pylint rules W0611, W0102, W1401, E1120, C0121, C0123, C0325, R0124, R1714.

* Fix f-strings and incorrect indentation levels

Address pylint rules W0311, W1309.

* Add pylint

* Rewrite serialization code with safer alternatives

Address Pylint rules W0123, R1722.

* fix sample script

* fix bug when standarizing data from Landgesell

* fix bug in peptide section of the tutorial

* clean-up output from tutorials

* Allow custom Python executables

* Comply with output directory flag from argparse

* fix on running globular_protein script

* Fix exit strategy

* remove not plot condition

* Fix unit system

* remove code repetition in standarize_data.py

---------

Co-authored-by: blancoapa <[email protected]>
Co-authored-by: blancoapa <[email protected]>
Co-authored-by: Pao <[email protected]>

.github/workflows/testsuite.yml

@@ -10,6 +10,9 @@ permissions:
 jobs:
   ubuntu:
     runs-on: ubuntu-latest
+    env:
+      FI_PROVIDER: "^psm3,psm3;ofi_rxd"
+      OMPI_MCA_mtl_ofi_provider_exclude: psm3
     steps:
       - name: Setup EESSI
         uses: eessi/github-action-eessi@v3
@@ -20,16 +23,17 @@ jobs:
       - name: Install dependencies
         run: |
           module load ESPResSo/4.2.1-foss-2023a
-          python3 -m venv --system-site-packages pymbe
-          source pymbe/bin/activate
+          python3 -m venv --system-site-packages venv
+          source venv/bin/activate
           python3 maintainer/configure_venv.py
           python3 -m pip install -r requirements.txt
-          python3 -m pip install "pdoc==14.3"
+          python3 -m pip install "pdoc==14.3" "pylint==3.0.3"
           deactivate
       - name: Run testsuite
         run: |
           module load ESPResSo/4.2.1-foss-2023a
-          source pymbe/bin/activate
+          source venv/bin/activate
+          make pylint
           make tests
           make docs
           deactivate

.pylintrc

@@ -0,0 +1,45 @@
+[MESSAGES CONTROL]
+
+# Only show warnings with the listed confidence levels. Leave empty to show
+# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED.
+confidence=
+
+# Disable the message, report, category or checker with the given id(s). You
+# can either give multiple identifiers separated by comma (,) or put this
+# option multiple times (only on the command line, not in the configuration
+# file where it should appear only once). You can also use "--disable=all" to
+# disable everything first and then reenable specific checks. For example, if
+# you want to run only the similarities checker, you can use "--disable=all
+# --enable=similarities". If you want to run only the classes checker, but have
+# no Warning level messages displayed, use "--disable=all --enable=classes
+# --disable=W".
+disable=all
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time (only on the command line, not in the configuration file where
+# it should appear only once). See also the "--disable" option for examples.
+enable=dangerous-default-value,        # W0102
+       duplicate-key,                  # W0109
+       eval-used,                      # W0123
+       assert-on-tuple,                # W0199
+       bad-indentation,                # W0311
+       wildcard-import,                # W0401
+       unused-import,                  # W0611
+       unused-variable,                # W0612
+       unused-argument,                # W0613
+       unused-wildcard-import,         # W0614
+       f-string-without-interpolation, # W1309
+       anomalous-backslash-in-string,  # W1401
+       deprecated-method,              # W1505
+       comparison-with-itself,         # R0124
+       cyclic-import,                  # R0401
+       trailing-comma-tuple,           # R1707
+       consider-using-in,              # R1714
+       consider-using-sys-exit,        # R1722
+       singleton-comparison,           # C0121
+       unidiomatic-typecheck,          # C0123
+       bad-classmethod-argument,       # C0202
+       superfluous-parens,             # C0325
+       undefined-variable,             # E0602
+       no-value-for-parameter,         # E1120

Makefile

@@ -3,32 +3,38 @@
 .PHONY: visual 
 .PHONY: clean
 
+PYTHON = python3
+
 docs:
 	mkdir -p ./documentation
-	pdoc ./pyMBE.py -o ./documentation --docformat google
+	PDOC_ALLOW_EXEC=0 ${PYTHON} -m pdoc ./pyMBE.py -o ./documentation --docformat google
 
 tests:
-	python3 testsuite/lj_tests.py
-	python3 testsuite/set_particle_acidity_test.py
-	python3 testsuite/bond_tests.py
-	python3 testsuite/generate_perpendicular_vectors_test.py
-	python3 testsuite/create_molecule_position_test.py
-	python3 testsuite/seed_test.py
-	python3 testsuite/read-write-df_test.py
-	python3 testsuite/parameter_test.py
-	python3 testsuite/henderson_hasselbalch_tests.py
-	python3 testsuite/cph_ideal_tests.py
-	python3 testsuite/grxmc_ideal_tests.py
-	python3 testsuite/peptide_tests.py
-	python3 testsuite/gcmc_tests.py
-	python3 testsuite/weak_polyelectrolyte_dialysis_test.py
-	python3 testsuite/globular_protein_tests.py
+	${PYTHON} testsuite/lj_tests.py
+	${PYTHON} testsuite/set_particle_acidity_test.py
+	${PYTHON} testsuite/bond_tests.py
+	${PYTHON} testsuite/generate_perpendicular_vectors_test.py
+	${PYTHON} testsuite/create_molecule_position_test.py
+	${PYTHON} testsuite/seed_test.py
+	${PYTHON} testsuite/read-write-df_test.py
+	${PYTHON} testsuite/parameter_test.py
+	${PYTHON} testsuite/henderson_hasselbalch_tests.py
+	${PYTHON} testsuite/cph_ideal_tests.py
+	${PYTHON} testsuite/grxmc_ideal_tests.py
+	${PYTHON} testsuite/peptide_tests.py
+	${PYTHON} testsuite/gcmc_tests.py
+	${PYTHON} testsuite/weak_polyelectrolyte_dialysis_test.py
+	${PYTHON} testsuite/globular_protein_tests.py
+
 sample:
-	python3 sample_scripts/peptide_simulation_example.py
+	${PYTHON} samples/peptide.py
 
 visual:
-	python3 handy_scripts/vmd-traj.py
+	${PYTHON} visualization/vmd-traj.py
 	vmd -e visualization.tcl
 
 tutorial:
 	jupyter-lab tutorials/pyMBE_tutorial.ipynb
+
+pylint:
+	${PYTHON} -m pylint pyMBE.py lib/ testsuite/ samples/ maintainer/ visualization/

lib/analysis.py

@@ -307,9 +307,9 @@ def get_dt(data):
     warn_lines = []
     for i in range(1,imax):
         dt = time[i] - time[i-1]
-        if(np.abs((dt_init - dt)/dt) > 0.01 ):
+        if np.abs((dt_init - dt)/dt) > 0.01:
             warn_lines.append("Row {} dt = {} = {} - {} not equal to dt_init = {}")
-    if(len(warn_lines) > 20):
+    if len(warn_lines) > 20:
         print("\n")
         for line in warn_lines:
             print(line)