Merge branch 'hackingmaterials:main' into fix_magwf_static_2

Author: fraricci

.circleci/config.yml

@@ -15,7 +15,7 @@ jobs:
             export PATH=$HOME/miniconda3/bin:$PATH
             conda create --name test_env python=3.8
             source activate test_env
-            conda install -c conda-forge openbabel pymatgen
+            conda install -c conda-forge openbabel gcc_linux-64
             pip install -r requirements-ci.txt
             pip install .
           no_output_timeout: 1h

.github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: Testing
+name: Tests
 
 on:
   push:
@@ -18,11 +18,15 @@ jobs:
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
+          cache: pip
+          cache-dependency-path: |
+            setup.py
+            requirements-ci.txt
           python-version: 3.8
 
       - name: Install OpenBabel
@@ -32,14 +36,6 @@ jobs:
           # https://github.com/openbabel/openbabel/issues/2408#issuecomment-1014466193
           sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3
 
-      - name: Cache pip
-        uses: actions/cache@v2
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements-ci.txt', 'setup.py') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
       - name: Install dependencies
         run: |
           pip install -r requirements-ci.txt

.pre-commit-config.yaml

@@ -1,36 +1,59 @@
+ci:
+  autoupdate_schedule: quarterly
+  skip: [mypy]
+
+default_stages: [commit]
+
+default_install_hook_types: [pre-commit, commit-msg]
+
 exclude: ^(docs/|.*test_files/|.*tests/)
 
 repos:
-  - repo: https://github.com/myint/autoflake
+  - repo: https://github.com/PyCQA/autoflake
     rev: v1.4
     hooks:
       - 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
+    rev: 22.6.0
     hooks:
       - id: black
 
-  - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
+  - repo: https://github.com/PyCQA/flake8
+    rev: 5.0.4
     hooks:
       - id: flake8
-        args: [--max-line-length=125]
+        additional_dependencies: [flake8-bugbear]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.971
+    hooks:
+      - id: mypy
+        additional_dependencies: [types-requests]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.3.0
     hooks:
+      - id: check-case-conflict
+      - id: check-symlinks
       - id: check-yaml
+      - id: destroyed-symlinks
       - id: end-of-file-fixer
+      - id: mixed-line-ending
       - id: trailing-whitespace
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.31.0
+    rev: v2.37.3
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
 
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.1
+    hooks:
+      - id: codespell
+        stages: [commit, commit-msg]
+
   - repo: https://github.com/PyCQA/isort
     rev: 5.10.1
     hooks:

README.md

@@ -1,10 +1,15 @@
-# <img alt="atomate" src="docs_rst/_static/atomate_logo_small.png" width="250">
+# <img alt="atomate" src="https://raw.githubusercontent.com/hackingmaterials/atomate/main/docs_rst/_static/atomate_logo_small.png" width="250">
+
+[![Tests](https://github.com/hackingmaterials/atomate/actions/workflows/test.yml/badge.svg)](https://github.com/hackingmaterials/atomate/actions/workflows/test.yml)
+[![PyPI Downloads](https://img.shields.io/pypi/dm/atomate?label=PyPI%20Downloads)](https://pypi.org/project/atomate)
+[![PyPI](https://img.shields.io/pypi/v/atomate?logo=pypi&logoColor=white)](https://pypi.org/project/atomate)
+[![Requires Python 3.8+](https://img.shields.io/badge/Python-3.8+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
 
 atomate is a software for computational materials science that contains pre-built workflows to compute and analyze the properties of materials.
 
-- **Website (including documentation):** https://hackingmaterials.github.io/atomate/
-- **Help/Support:** https://discuss.matsci.org/c/atomate
-- **Source:** https://github.com/hackingmaterials/atomate
+- **Website (including documentation):** <https://hackingmaterials.github.io/atomate/>
+- **Help/Support:** <https://discuss.matsci.org/c/atomate>
+- **Source:** <https://github.com/hackingmaterials/atomate>
 
 If you find atomate useful, please encourage its development by citing the following paper in your research output:
 

atomate/__init__.py

@@ -1 +1 @@
-__version__ = "1.0.2"
+__version__ = "1.0.3"

atomate/common/firetasks/glue_tasks.py

@@ -95,10 +95,17 @@ class CopyFilesFromCalcLoc(FiretaskBase):
         name_append (str): string to append to destination filenames.
         exclude_files (list): list of file names to be excluded. Accepts glob
             patterns.
+        decompress (bool): if True, files are decompressed after copy.
     """
 
     required_params = ["calc_loc"]
-    optional_params = ["filenames", "name_prepend", "name_append", "exclude_files"]
+    optional_params = [
+        "filenames",
+        "name_prepend",
+        "name_append",
+        "exclude_files",
+        "decompress",
+    ]
 
     def run_task(self, fw_spec=None):
         calc_loc = get_calc_loc(self["calc_loc"], fw_spec["calc_locs"])
@@ -142,10 +149,15 @@ def run_task(self, fw_spec=None):
 
         for f in files_to_copy:
             prev_path_full = os.path.join(calc_dir, f)
-            dest_fname = self.get("name_prepend", "") + f + self.get("name_append", "")
+            f, ext = os.path.splitext(f)
+            dest_fname = (
+                self.get("name_prepend", "") + f + self.get("name_append", "") + ext
+            )
             dest_path = os.path.join(os.getcwd(), dest_fname)
 
             fileclient.copy(prev_path_full, dest_path)
+            if self.get("decompress", False):
+                monty.shutil.decompress_file(dest_path)
 
 
 @explicit_serialize

atomate/common/powerups.py

@@ -61,14 +61,18 @@ def add_tags(original_wf, tags_list):
 
     # WF metadata
     if "tags" in original_wf.metadata:
-        original_wf.metadata["tags"].extend(tags_list)
+        for t in tags_list:
+            if t not in original_wf.metadata["tags"]:
+                original_wf.metadata["tags"].append(t)
     else:
         original_wf.metadata["tags"] = tags_list
 
     # FW metadata
     for idx_fw in range(len(original_wf.fws)):
         if "tags" in original_wf.fws[idx_fw].spec:
-            original_wf.fws[idx_fw].spec["tags"].extend(tags_list)
+            for t in tags_list:
+                if t not in original_wf.fws[idx_fw].spec["tags"]:
+                    original_wf.fws[idx_fw].spec["tags"].append(t)
         else:
             original_wf.fws[idx_fw].spec["tags"] = tags_list
 
@@ -77,9 +81,16 @@ def add_tags(original_wf, tags_list):
     for idx_fw, idx_t in idxs:
         if "additional_fields" in original_wf.fws[idx_fw].tasks[idx_t].optional_params:
             if "tags" in original_wf.fws[idx_fw].tasks[idx_t]["additional_fields"]:
-                original_wf.fws[idx_fw].tasks[idx_t]["additional_fields"][
-                    "tags"
-                ].extend(tags_list)
+                for t in tags_list:
+                    if (
+                        t
+                        not in original_wf.fws[idx_fw].tasks[idx_t][
+                            "additional_fields"
+                        ]["tags"]
+                    ):
+                        original_wf.fws[idx_fw].tasks[idx_t]["additional_fields"][
+                            "tags"
+                        ].append(t)
             else:
                 original_wf.fws[idx_fw].tasks[idx_t]["additional_fields"][
                     "tags"

atomate/feff/workflows/tests/test_eels_workflows.py

@@ -14,9 +14,8 @@
 
 module_dir = os.path.dirname(os.path.abspath(__file__))
 db_dir = os.path.join(module_dir, "..", "..", "..", "common", "test_files")
-DEBUG_MODE = (
-    False  # If true, retains the database and output dirs at the end of the test
-)
+# If DEBUG_MODE = true, retains the database and output dirs at the end of the test
+DEBUG_MODE = False
 
 
 class TestEELSWorkflow(AtomateTest):

atomate/feff/workflows/tests/test_exafs_scattering_paths.py

@@ -41,7 +41,6 @@ def test_feff_input_sets(self):
             "nkpts": 1000,
             "radius": 10.0,
             "user_tag_settings": {},
-            "structure": self.struct.as_dict(),
         }
         ans_fis_fw2 = {
             "@class": "MPEXAFSSet",
@@ -51,13 +50,14 @@ def test_feff_input_sets(self):
             "nkpts": 1000,
             "radius": 10.0,
             "user_tag_settings": {"CONTROL": "0 0 0 0 1 1", "PRINT": "0 0 0 1 0 3"},
-            "structure": self.struct.as_dict(),
         }
         fis_fw1 = self.fw1_dict["spec"]["_tasks"][0]["feff_input_set"]
         fis_fw2 = self.fw2_dict["spec"]["_tasks"][1]["feff_input_set"]
 
         fis_fw1.pop("@version")
         fis_fw2.pop("@version")
+        fis_fw1.pop("structure")
+        fis_fw2.pop("structure")
 
         self.assertDictEqual(fis_fw1, ans_fis_fw1)
         self.assertDictEqual(fis_fw2, ans_fis_fw2)

atomate/feff/workflows/tests/test_xas_workflows.py

@@ -16,9 +16,8 @@
 module_dir = os.path.dirname(os.path.abspath(__file__))
 db_dir = os.path.join(module_dir, "..", "..", "..", "common", "test_files")
 
-DEBUG_MODE = (
-    False  # If true, retains the database and output dirs at the end of the test
-)
+# If DEBUG_MODE = true, retains the database and output dirs at the end of the test
+DEBUG_MODE = False
 FEFF_CMD = None  # "feff"