Merge remote-tracking branch 'hackmat/main' into qchem_update

Author: espottesmith

.circleci/config.yml

@@ -4,7 +4,7 @@ jobs:
     working_directory: ~/atomate
     docker:
       - image: materialsvirtuallab/circle-ci-pmg-py3:3.7.3
-      - image: circleci/mongo:3.4.15
+      - image: circleci/mongo:latest
     steps:
       - checkout
       - restore_cache:
@@ -37,7 +37,7 @@ jobs:
     working_directory: ~/atomate
     docker:
       - image: materialsvirtuallab/circle-ci-pmg-py3:3.7.3
-      - image: circleci/mongo:3.4.15
+      - image: circleci/mongo:latest
     steps:
       - checkout
       - restore_cache:
@@ -56,9 +56,6 @@ jobs:
             tar -zxvf vampire-5.0-linux.tar.gz
             export PATH=/root/atomate/linux/:$PATH
             pip install --quiet -r requirements.txt -r requirements-ci.txt
-            pip install git+https://github.com/materialsproject/pymatgen.git --upgrade
-            pip install git+https://github.com/materialsproject/custodian.git --upgrade
-            pip install git+https://github.com/materialsproject/fireworks.git --upgrade
             # Add executables and path.
             for EXEPATH in `pwd`/cmd_line/*/Linux_64bit; do export PATH=$PATH:$EXEPATH; done
             pip install --quiet -e .
@@ -76,9 +73,7 @@ workflows:
     jobs:
       - py3test
       - py3devtest:
-          filters:  # don't run dev tests on master branch
+          filters:  # don't run dev tests on main branch
               branches:
                   ignore:
-                      master
-
-
+                      main

.github/workflows/test.yml

@@ -0,0 +1,44 @@
+name: Testing
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      - name: Install C++ dependencies
+        run: |
+          sudo apt-get install openbabel
+
+      - name: Cache pip
+        uses: actions/cache@v2
+        id: pip-cache
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        if: steps.pip-cache.outputs.cache-hit != 'true'
+        run: |
+          pip install -r requirements.txt
+          pip install -r requirements-ci.txt
+          pip install .[complete]
+
+      - name: pytest
+        run: |
+          pytest --ignore=atomate/qchem/test_files --cov=atomate --cov-report html:coverage_reports atomate

.gitignore

@@ -44,8 +44,8 @@ nosetests.xml
 
 # Pycharm
 .idea/*
-
 .eggs/*
+venv
 
 # VS Code
 settings.json

.pre-commit-config.yaml

@@ -1,19 +1,30 @@
 repos:
-  - repo: git@github.com:humitos/mirrors-autoflake.git
-    rev: v1.1
+  - repo: https://github.com/myint/autoflake
+    rev: v1.4
     hooks:
-    - id: autoflake
-      args: [ '--in-place', '--remove-all-unused-imports', '--remove-unused-variable' ]
-  - repo: https://github.com/ambv/black
-    rev: stable
+      - id: autoflake
+        args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
+
+  - repo: https://github.com/psf/black
+    rev: 21.11b1
     hooks:
-    - id: black
-      language_version: python3.7
+      - id: black
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        args: [--max-line-length=125]
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v4.0.1
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-      - id: flake8
-        args: ["--max-line-length=125"]
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.31.0
+    hooks:
+      - id: pyupgrade
+        args: [--py37-plus]

CONTRIBUTING.md

@@ -1,15 +1,19 @@
 # Contributing to atomate
+
 We love your input! We want to make contributing to atomate as easy and transparent as possible, whether it's:
+
 * Reporting a bug
 * Discussing the current state of the code
 * Submitting a fix
 * Proposing or implementing new features
 * Becoming a maintainer
 
 ## Reporting bugs, getting help, and discussion
+
 At any time, feel free to start a thread on our [Discourse forum](https://discuss.matsci.org/c/atomate).
 
 If you are making a bug report, incorporate as many elements of the following as possible to ensure a timely response and avoid the need for followups:
+
 * A quick summary and/or background
 * Steps to reproduce - be specific! **Provide sample code.**
 * What you expected would happen, compared to what actually happens
@@ -19,16 +23,19 @@ If you are making a bug report, incorporate as many elements of the following as
 We love thorough bug reports as this means the development team can make quick and meaningful fixes. When we confirm your bug report, we'll move it to the GitHub issues where its progress can be further tracked.
 
 ## Contributing code modifications or additions through Github
-We use github to host code, to track issues and feature requests, as well as accept pull requests. We maintain a list of all contributors to atomate [here.](https://atomate.org/contributors.html)
+
+We use github to host code, to track issues and feature requests, as well as accept pull requests. We maintain a list of all contributors to atomate [here](https://atomate.org/contributors.html).
 
 Pull requests are the best way to propose changes to the codebase. Follow the [Github flow](https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow) for more information on this procedure.
 
 The basic procedure for making a PR is:
-* Fork the repo and create your branch from master.
+
+* Fork the repo and create your branch from main.
 * Commit your improvements to your branch and push to your Github fork (repo).
 * When you're finished, go to your fork and make a Pull Request. It will automatically update if you need to make further changes.
 
 ### How to Make a **Great** Pull Request
+
 We have a few tips for writing good PRs that are accepted into the main repo:
 
 * Use the Google Code style for all of your code. Find an example [here.](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html)
@@ -41,4 +48,5 @@ When you submit your PR, our CI service will automatically run your tests.
 We welcome good discussion on the best ways to write your code, and the comments on your PR are an excellent area for discussion.
 
 #### References
+
 This document was adapted from the open-source contribution guidelines for Facebook's Draft, as well as briandk's [contribution template](https://gist.github.com/briandk/3d2e8b3ec8daf5a27a62).

atomate/__init__.py

@@ -1 +1 @@
-__version__ = "0.9.5"
+__version__ = "1.0.1"

atomate/common/__init__.py

@@ -1 +1 @@
-__author__ = 'Anubhav Jain <[email protected]>'
+__author__ = "Anubhav Jain <[email protected]>"

atomate/common/firetasks/__init__.py

@@ -1 +1 @@
-__author__ = 'Anubhav Jain <[email protected]>'
+__author__ = "Anubhav Jain <[email protected]>"

atomate/common/firetasks/glue_tasks.py

@@ -1,6 +1,3 @@
-# coding: utf-8
-
-
 import os
 import monty
 import shutil
@@ -72,7 +69,7 @@ def get_calc_loc(target_name, calc_locs):
         for doc in reversed(calc_locs):
             if doc["name"] == target_name:
                 return doc
-        raise ValueError("Could not find the target_name: {}".format(target_name))
+        raise ValueError(f"Could not find the target_name: {target_name}")
     else:
         return calc_locs[-1]
 

atomate/common/firetasks/parse_outputs.py

@@ -1,16 +1,12 @@
-# coding: utf-8
-
-
 import json
 import os
 
-from fireworks import explicit_serialize, FiretaskBase, FWAction
-from fireworks.utilities.fw_serializers import DATETIME_HANDLER
-
-from atomate.utils.utils import env_chk, get_logger, load_class
 from atomate.common.firetasks.glue_tasks import get_calc_loc
+from atomate.utils.utils import env_chk, get_logger, load_class
+from fireworks import FiretaskBase, FWAction, explicit_serialize
+from fireworks.utilities.fw_serializers import DATETIME_HANDLER
 
-__author__ = 'Shyam Dwaraknath <[email protected]>, Anubhav Jain <[email protected]>'
+__author__ = "Shyam Dwaraknath <[email protected]>, Anubhav Jain <[email protected]>"
 
 logger = get_logger(__name__)
 
@@ -37,7 +33,14 @@ class ToDbTask(FiretaskBase):
     """
 
     required_params = ["drone"]
-    optional_params = ["mmdb", "db_file", "calc_dir", "calc_loc", "additional_fields", "options"]
+    optional_params = [
+        "mmdb",
+        "db_file",
+        "calc_dir",
+        "calc_loc",
+        "additional_fields",
+        "options",
+    ]
 
     def run_task(self, fw_spec):
         # get the directory that contains the dir to parse
@@ -48,12 +51,13 @@ def run_task(self, fw_spec):
             calc_dir = get_calc_loc(self["calc_loc"], fw_spec["calc_locs"])["path"]
 
         # parse the calc directory
-        logger.info("PARSING DIRECTORY: {} USING DRONE: {}".format(
-            calc_dir, self['drone'].__class__.__name__))
+        logger.info(
+            f"PARSING DIRECTORY: {calc_dir} USING DRONE: {self['drone'].__class__.__name__}"
+        )
         # get the database connection
-        db_file = env_chk(self.get('db_file'), fw_spec)
+        db_file = env_chk(self.get("db_file"), fw_spec)
 
-        drone = self['drone'].__class__()
+        drone = self["drone"].__class__()
         task_doc = drone.assimilate(calc_dir)
         if not db_file:
             with open("task.json", "w") as f:
@@ -66,7 +70,9 @@ def run_task(self, fw_spec):
 
             # insert the task document
             t_id = db.insert(task_doc)
-            logger.info("Finished parsing with task_id: {}".format(t_id))
+            logger.info(f"Finished parsing with task_id: {t_id}")
 
-        return FWAction(stored_data={"task_id": task_doc.get("task_id", None)},
-                        defuse_children=(task_doc["state"] != "successful"))
+        return FWAction(
+            stored_data={"task_id": task_doc.get("task_id", None)},
+            defuse_children=(task_doc["state"] != "successful"),
+        )