Merge pull request #738 from janosh/py38+

Drop py37 support

Author: Zhuoying

.circleci/config.yml

@@ -1,66 +1,30 @@
-version: 2
+version: 2.1
 jobs:
-  py3test:
+  test:
     working_directory: ~/atomate
     docker:
-      - image: materialsvirtuallab/circle-ci-pmg-py3:3.7.3
-      - image: circleci/mongo:latest
+      - image: continuumio/miniconda3
+      - image: circleci/mongo
     steps:
       - checkout
       - restore_cache:
-          key: deps1-{{ .Branch }}-{{ checksum "requirements.txt" }}
+          key: deps-{{ checksum "requirements-ci.txt" }}-{{ checksum "setup.py" }}
       - run:
+          name: Install dependencies
           command: |
             export PATH=$HOME/miniconda3/bin:$PATH
-            conda create --quiet --yes --name test_env python=3.7
+            conda create --name test_env python=3.8
             source activate test_env
-            conda install --quiet --yes numpy scipy matplotlib sympy pandas
-            conda install --quiet --yes -c conda-forge openbabel
-            # conda install --quiet --yes -c clinicalgraphics vtk
-            conda install --quiet --yes -c conda-forge python-igraph
-            conda update --quiet --all
-            wget https://vampire.york.ac.uk/resources/release-5/vampire-5.0-linux.tar.gz
-            tar -zxvf vampire-5.0-linux.tar.gz
-            export PATH=/root/atomate/linux/:$PATH
-            pip install --quiet -r requirements.txt -r requirements-ci.txt
-            # Add executables and path.
-            for EXEPATH in `pwd`/cmd_line/*/Linux_64bit; do export PATH=$PATH:$EXEPATH; done
-            pip install --quiet -e .
-            pytest --ignore=atomate/qchem/test_files --cov=atomate --cov-report html:coverage_reports atomate
-          no_output_timeout: 3600
-      - store_artifacts:
-          path: coverage_reports/
-          destination: tr1
-      - store_test_results:
-          path: coverage_reports/
-  py3devtest:
-    working_directory: ~/atomate
-    docker:
-      - image: materialsvirtuallab/circle-ci-pmg-py3:3.7.3
-      - image: circleci/mongo:latest
-    steps:
-      - checkout
-      - restore_cache:
-          key: deps1-{{ .Branch }}-{{ checksum "requirements.txt" }}
+            conda install -c conda-forge openbabel pymatgen
+            pip install -r requirements-ci.txt
+            pip install .
+          no_output_timeout: 1h
       - run:
+          name: pytest
           command: |
-            export PATH=$HOME/miniconda3/bin:$PATH
-            conda create --quiet --yes --name test_env python=3.7
             source activate test_env
-            conda install --quiet --yes numpy scipy matplotlib sympy pandas
-            conda install --quiet --yes -c conda-forge openbabel
-            # conda install --quiet --yes -c clinicalgraphics vtk
-            conda install --quiet --yes -c conda-forge python-igraph
-            conda update --quiet --all
-            wget https://vampire.york.ac.uk/resources/release-5/vampire-5.0-linux.tar.gz
-            tar -zxvf vampire-5.0-linux.tar.gz
-            export PATH=/root/atomate/linux/:$PATH
-            pip install --quiet -r requirements.txt -r requirements-ci.txt
-            # Add executables and path.
-            for EXEPATH in `pwd`/cmd_line/*/Linux_64bit; do export PATH=$PATH:$EXEPATH; done
-            pip install --quiet -e .
             pytest --ignore=atomate/qchem/test_files --cov=atomate --cov-report html:coverage_reports atomate
-          no_output_timeout: 3600
+          no_output_timeout: 1h
       - store_artifacts:
           path: coverage_reports/
           destination: tr1
@@ -71,9 +35,4 @@ workflows:
   version: 2
   build_and_test:
     jobs:
-      - py3test
-      - py3devtest:
-          filters:  # don't run dev tests on main branch
-              branches:
-                  ignore:
-                      main
+      - test

.github/workflows/test.yml

@@ -23,7 +23,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install OpenBabel
         run: |

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
     rev: v2.31.0
     hooks:
       - id: pyupgrade
-        args: [--py37-plus]
+        args: [--py38-plus]
 
   - repo: https://github.com/PyCQA/isort
     rev: 5.10.1

README.md

@@ -8,7 +8,7 @@ atomate is a software for computational materials science that contains pre-buil
 
 If you find atomate useful, please encourage its development by citing the following paper in your research output:
 
-```
+```txt
 Mathew, K., Montoya, J. H., Faghaninia, A., Dwarakanath, S., Aykol,
 M., Tang, H., Chu, I., Smidt, T., Bocklund, B., Horton, M., Dagdelen,
 J., Wood, B., Liu, Z.-K., Neaton, J., Ong, S. P., Persson, K., Jain,

atomate/common/powerups.py

@@ -1,6 +1,7 @@
 """
 This module defines general powerups that can be used for all workflows
 """
+
 from importlib import import_module
 from typing import List
 

atomate/feff/workflows/core.py

@@ -87,9 +87,8 @@ def get_wf_xas(
 
     wf_metadata = dict(metadata) if metadata else {}
     wf_metadata["absorbing_atom_indices"] = list(ab_atom_indices)
-    wfname = "{}:{}:{} edge".format(
-        structure.composition.reduced_formula, f"{spectrum_type} spectroscopy", edge
-    )
+    formula = structure.composition.reduced_formula
+    wfname = f"{formula}:{spectrum_type} spectroscopy:{edge} edge"
 
     return Workflow(fws, name=wfname, metadata=wf_metadata)
 
@@ -257,9 +256,8 @@ def get_wf_eels(
             )
         )
 
-    wfname = "{}:{}:{} edge".format(
-        structure.composition.reduced_formula, f"{spectrum_type} spectroscopy", edge
-    )
+    formula = structure.composition.reduced_formula
+    wfname = f"{formula}:{spectrum_type} spectroscopy:{edge} edge"
     wf_metadata = dict(metadata) if metadata else {}
     wf_metadata["absorbing_atom_indices"] = list(ab_atom_indices)
 

atomate/lammps/firetasks/run_calc.py

@@ -95,7 +95,7 @@ def run_task(self, fw_spec):
             output_file=self.get("output_file", "packed_mol.xyz"),
             bin=self["packmol_cmd"],
         )
-        logger.info("Running {}".format(self["packmol_cmd"]))
+        logger.info(f"Running {self['packmol_cmd']}")
         packed_mol = pmr.run(site_property=self.get("site_property", None))
         logger.info("Packmol finished running.")
         return FWAction(mod_spec=[{"_set": {"packed_mol": packed_mol}}])

atomate/qchem/workflows/base/FF_and_critic.py

@@ -62,9 +62,7 @@ def get_wf_FFopt_and_critic(
     # FFopt
     fw1 = FrequencyFlatteningOptimizeFW(
         molecule=molecule,
-        name="{}:{}".format(
-            molecule.composition.alphabetical_formula, "FFopt_" + suffix
-        ),
+        name=f"{molecule.composition.alphabetical_formula}:{'FFopt_' + suffix}",
         qchem_cmd=">>qchem_cmd<<",
         max_cores=">>max_cores<<",
         qchem_input_params=qchem_input_params,
@@ -74,7 +72,7 @@ def get_wf_FFopt_and_critic(
 
     # Critic
     fw2 = CubeAndCritic2FW(
-        name="{}:{}".format(molecule.composition.alphabetical_formula, "CC2_" + suffix),
+        name=f"{molecule.composition.alphabetical_formula}:{'CC2_' + suffix}",
         qchem_cmd=">>qchem_cmd<<",
         max_cores=">>max_cores<<",
         qchem_input_params=qchem_input_params,
@@ -83,8 +81,6 @@ def get_wf_FFopt_and_critic(
     )
     fws = [fw1, fw2]
 
-    wfname = "{}:{}".format(
-        molecule.composition.alphabetical_formula, "FFopt_CC2_WF_" + suffix
-    )
+    wfname = f"{molecule.composition.alphabetical_formula}:{'FFopt_CC2_WF_' + suffix}"
 
     return Workflow(fws, name=wfname, **kwargs)

atomate/qchem/workflows/base/torsion_potential.py

@@ -98,13 +98,8 @@ def get_wf_torsion_potential(
         rot_task = RotateTorsion(atom_indexes=atom_indexes, angle=angle)
         rot_opt_fw.tasks.insert(0, rot_task)
         # define opt section
-        opt_line = "tors {a} {b} {c} {d} {ang}".format(
-            a=atom_indexes[0],
-            b=atom_indexes[1],
-            c=atom_indexes[2],
-            d=atom_indexes[3],
-            ang=angle,
-        )
+        a, b, c, d = atom_indexes
+        opt_line = f"tors {a} {b} {c} {d} {angle}"
         opt = {"CONSTRAINT": [opt_line]}
         for idx_t, t in enumerate(rot_opt_fw.tasks):
             if "WriteInputFromIOSet" in str(t):

atomate/qchem/workflows/tests/test_FF_and_critic.py

@@ -49,13 +49,14 @@ def test_FFopt_and_critic(self):
             },
         )
         # use powerup to replace run with fake run
+        alph_formula = initial_mol.composition.alphabetical_formula
         ref_dirs = {
-            "{}:{}".format(
-                initial_mol.composition.alphabetical_formula, "FFopt_testing"
-            ): os.path.join(test_files, "FFopt"),
-            "{}:{}".format(
-                initial_mol.composition.alphabetical_formula, "CC2_testing"
-            ): os.path.join(test_files, "critic_example"),
+            f"{alph_formula}:FFopt_testing": os.path.join(
+                test_files, "FFopt"
+            ),
+            f"{alph_formula}:CC2_testing": os.path.join(
+                test_files, "critic_example"
+            ),
         }
         fake_wf = use_fake_qchem(real_wf, ref_dirs)
         self.lp.add_wf(fake_wf)
@@ -70,22 +71,14 @@ def test_FFopt_and_critic(self):
         self.assertTrue(all([s == "COMPLETED" for s in wf_test.fw_states.values()]))
 
         FFopt = self.get_task_collection().find_one(
-            {
-                "task_label": "{}:{}".format(
-                    initial_mol.composition.alphabetical_formula, "FFopt_testing"
-                )
-            }
+            {"task_label": f"{alph_formula}:FFopt_testing"}
         )
         self.assertEqual(FFopt["calcs_reversed"][0]["input"]["smx"]["solvent"], "other")
         self.assertEqual(FFopt["num_frequencies_flattened"], 0)
         FFopt_final_mol = Molecule.from_dict(FFopt["output"]["optimized_molecule"])
 
         CC2 = self.get_task_collection().find_one(
-            {
-                "task_label": "{}:{}".format(
-                    initial_mol.composition.alphabetical_formula, "CC2_testing"
-                )
-            }
+            {"task_label": f"{alph_formula}:CC2_testing"}
         )
         CC2_initial_mol = Molecule.from_dict(CC2["input"]["initial_molecule"])