Merge branch 'master' into Parsing_zval_Psf_Psml

.readthedocs.yml

@@ -3,10 +3,10 @@ version: 2
 python:
     version: 3.8
     install:
-        -   method: pip
-            path: .
-            extra_requirements:
-            -   docs
+    -   method: pip
+        path: .
+        extra_requirements:
+        -   docs
 
 sphinx:
     builder: html

docs/source/conf.py

@@ -4,24 +4,15 @@
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-import os
-import sys
-
-sys.path.insert(0, os.path.abspath('../../'))
-
 import aiida_pseudo
 
 # -- Project information -----------------------------------------------------
 
 project = 'aiida-pseudo'
-copyright = '2020-2021, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland'
+copyright = """\
+2020-2022, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre
+for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland
+"""
 release = aiida_pseudo.__version__
 
 # -- General configuration ---------------------------------------------------

pyproject.toml

@@ -116,12 +116,6 @@ minversion = '6.0'
 testpaths = [
     'tests',
 ]
-filterwarnings = [
-    'ignore::DeprecationWarning:distutils:',
-    'ignore::DeprecationWarning:frozendict:',
-    'ignore::DeprecationWarning:sqlalchemy_utils:',
-    'ignore::DeprecationWarning:pkg_resources:',
-]
 
 [tool.yapf]
 align_closing_bracket_with_visual_indent = true

src/aiida_pseudo/cli/install.py

@@ -23,7 +23,7 @@ def cmd_install():
 
 
 @cmd_install.command('family')
-@click.argument('archive', type=types.PathOrUrl(exists=True, file_okay=True))
+@click.argument('archive', type=types.PathOrUrl(exists=True, file_okay=True, path_type=pathlib.Path))
 @click.argument('label', type=click.STRING)
 @options_core.DESCRIPTION(help='Description for the family.')
 @options.ARCHIVE_FORMAT()

src/aiida_pseudo/cli/utils.py

@@ -53,13 +53,12 @@ def create_family_from_archive(cls, label, filepath_archive: Path, fmt=None, pse
     with tempfile.TemporaryDirectory() as dirpath:
 
         try:
-            # In Python 3.6 the ``unpack_archive`` method does not yet support ``pathlib.Path`` objects.
-            shutil.unpack_archive(str(filepath_archive), dirpath, format=fmt)
+            shutil.unpack_archive(filepath_archive, dirpath, format=fmt)
         except shutil.ReadError as exception:
             raise OSError(f'failed to unpack the archive `{filepath_archive}`: {exception}') from exception
 
         try:
-            family = cls.create_from_folder(dirpath, label, pseudo_type=pseudo_type)
+            family = cls.create_from_folder(Path(dirpath), label, pseudo_type=pseudo_type)
         except ValueError as exception:
             raise OSError(f'failed to parse pseudos from `{dirpath}`: {exception}') from exception
 

src/aiida_pseudo/groups/family/pseudo.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
 """Subclass of ``Group`` that serves as a base class for representing pseudo potential families."""
-import os
 import re
 from typing import List, Mapping, Tuple, Union
 
@@ -77,13 +76,13 @@ def _validate_dirpath(cls, dirpath):
 
         :return: the directory path to be used.
         """
-        if not os.path.isdir(dirpath):
+        if not dirpath.is_dir():
             raise ValueError(f'`{dirpath}` is not a directory')
 
-        dirpath_contents = os.listdir(dirpath)
+        dirpath_contents = list(dirpath.iterdir())
 
-        if len(dirpath_contents) == 1 and os.path.isdir(os.path.join(dirpath, dirpath_contents[0])):
-            dirpath = os.path.join(dirpath, dirpath_contents[0])
+        if len(dirpath_contents) == 1 and (dirpath / dirpath_contents[0]).is_dir():
+            dirpath = dirpath_contents[0]
 
         return dirpath
 
@@ -115,11 +114,12 @@ def parse_pseudos_from_directory(cls, dirpath, pseudo_type=None, deduplicate=Tru
         dirpath = cls._validate_dirpath(dirpath)
         pseudo_type = cls._validate_pseudo_type(pseudo_type)
 
-        for filename in os.listdir(dirpath):
-            filepath = os.path.join(dirpath, filename)
+        for filepath in dirpath.iterdir():
 
-            if not os.path.isfile(filepath):
-                raise ValueError(f'dirpath `{dirpath}` contains at least one entry that is not a file')
+            filename = filepath.name
+
+            if not filepath.is_file():
+                raise ValueError(f'dirpath `{dirpath}` contains at least one entry that is not a file: {filepath}')
 
             with open(filepath, 'rb') as handle:
                 try:

src/aiida_pseudo/groups/family/pseudo_dojo.py

@@ -1,8 +1,7 @@
 # -*- coding: utf-8 -*-
 """Subclass of `PseudoPotentialFamily` designed to represent a PseudoDojo configuration."""
 import json
-import os
-from pathlib import Path
+import pathlib
 import re
 from typing import NamedTuple, Sequence
 import warnings
@@ -247,7 +246,7 @@ def get_cutoffs_from_djrepo(cls, djrepo, pseudo_type):
         return cutoffs
 
     @classmethod
-    def parse_djrepos_from_folder(cls, dirpath, pseudo_type):
+    def parse_djrepos_from_folder(cls, dirpath: pathlib.Path, pseudo_type):
         # pylint: disable=too-many-locals,too-many-branches
         """Parse the djrepo files in the given directory into a list of data nodes.
 
@@ -265,19 +264,14 @@ def parse_djrepos_from_folder(cls, dirpath, pseudo_type):
         cutoffs = {'low': {}, 'normal': {}, 'high': {}}
         elements = []
 
-        if not os.path.isdir(dirpath):
-            raise ValueError(f'`{dirpath}` is not a directory')
+        dirpath = cls._validate_dirpath(dirpath)
 
-        dirpath_contents = os.listdir(dirpath)
+        for filepath in dirpath.iterdir():
 
-        if len(dirpath_contents) == 1 and os.path.isdir(os.path.join(dirpath, dirpath_contents[0])):
-            dirpath = os.path.join(dirpath, dirpath_contents[0])
+            filename = filepath.name
 
-        for filename in os.listdir(dirpath):
-            filepath = os.path.join(dirpath, filename)
-
-            if not os.path.isfile(filepath):
-                raise ValueError(f'dirpath `{dirpath}` contains at least one entry that is not a file')
+            if not filepath.is_file():
+                raise ValueError(f'dirpath `{dirpath}` contains at least one entry that is not a file: {filepath}')
 
             # Some of the djrepo archives contain extraneous files. Here we skip files with unsupported extensions.
             if filename.split('.')[-1] not in cls._pseudo_repo_file_extensions:
@@ -325,7 +319,7 @@ def parse_djrepos_from_folder(cls, dirpath, pseudo_type):
         return md5s, cutoffs
 
     @classmethod
-    def parse_djrepos_from_archive(cls, filepath_metadata: Path, fmt=None, pseudo_type=None):
+    def parse_djrepos_from_archive(cls, filepath_metadata: pathlib.Path, fmt=None, pseudo_type=None):
         """Parse metadata from a djrepo .tgz archive.
 
         .. warning:: the archive should not contain any subdirectories, but just the djrepo files.
@@ -344,15 +338,14 @@ def parse_djrepos_from_archive(cls, filepath_metadata: Path, fmt=None, pseudo_ty
 
         with tempfile.TemporaryDirectory() as dirpath:
             try:
-                # In Python 3.6 the ``unpack_archive`` method does not yet support ``pathlib.Path`` objects.
-                shutil.unpack_archive(str(filepath_metadata), dirpath, format=fmt)
+                shutil.unpack_archive(filepath_metadata, dirpath, format=fmt)
             except shutil.ReadError as exception:
                 raise OSError(
                     f'failed to unpack the metadata archive `{filepath_metadata}`: {exception}'
                 ) from exception
 
             try:
-                md5s, cutoffs = cls.parse_djrepos_from_folder(dirpath, pseudo_type=pseudo_type)
+                md5s, cutoffs = cls.parse_djrepos_from_folder(pathlib.Path(dirpath), pseudo_type=pseudo_type)
             except ValueError as exception:
                 raise OSError(f'failed to parse djrepos from `{dirpath}`: {exception}') from exception
 

tests/cli/test_install.py

@@ -15,7 +15,7 @@
 
 
 @pytest.fixture
-def run_monkeypatched_install_sssp(run_cli_command, get_pseudo_potential_data, monkeypatch, tmpdir):
+def run_monkeypatched_install_sssp(run_cli_command, get_pseudo_potential_data, monkeypatch, tmp_path):
     """Fixture to monkeypatch the ``aiida_pseudo.cli.install.download_sssp`` method and call the install cmd."""
 
     def download_sssp(
@@ -37,14 +37,14 @@ def download_sssp(
 
         element = 'Ar'
         pseudo = get_pseudo_potential_data(element)
-        filepath = tmpdir / pseudo.filename
+        filepath = tmp_path / pseudo.filename
 
         with pseudo.open(mode='rb') as handle:
             md5 = hashlib.md5(handle.read()).hexdigest()
             handle.seek(0)
-            filepath.write_binary(handle.read())
+            filepath.write_bytes(handle.read())
 
-        filename_archive = shutil.make_archive('temparchive', 'gztar', root_dir=tmpdir, base_dir='.')
+        filename_archive = shutil.make_archive('temparchive', 'gztar', root_dir=tmp_path, base_dir='.')
         shutil.move(pathlib.Path.cwd() / filename_archive, filepath_archive)
 
         with open(filepath_metadata, 'w', encoding='utf-8') as handle:
@@ -60,7 +60,7 @@ def _run_monkeypatched_install_sssp(options=None, raises=None):
 
 
 @pytest.fixture
-def run_monkeypatched_install_pseudo_dojo(run_cli_command, get_pseudo_potential_data, monkeypatch, tmpdir):
+def run_monkeypatched_install_pseudo_dojo(run_cli_command, get_pseudo_potential_data, monkeypatch, tmp_path):
     """Fixture to monkeypatch the ``aiida_pseudo.cli.install.download_pseudo_dojo`` method and call the install cmd."""
 
     def download_pseudo_dojo(
@@ -82,25 +82,25 @@ def download_pseudo_dojo(
 
         element = 'Ar'
         pseudo = get_pseudo_potential_data(element, entry_point='jthxml')
-        filepath = tmpdir / pseudo.filename
+        filepath = tmp_path / pseudo.filename
 
         with pseudo.open(mode='rb') as handle:
             md5 = hashlib.md5(handle.read()).hexdigest()
             handle.seek(0)
-            filepath.write_binary(handle.read())
+            filepath.write_bytes(handle.read())
 
-        filename_archive = shutil.make_archive('temparchive', 'gztar', root_dir=tmpdir, base_dir='.')
+        filename_archive = shutil.make_archive('temparchive', 'gztar', root_dir=tmp_path, base_dir='.')
         shutil.move(pathlib.Path.cwd() / filename_archive, filepath_archive)
 
         data = {'hints': {'high': {'ecut': 20.00}, 'low': {'ecut': 20.00}, 'normal': {'ecut': 20.00}}, 'md5': md5}
 
-        filepath_djrepo = tmpdir / f'{element}.djrepo'
+        filepath_djrepo = tmp_path / f'{element}.djrepo'
 
         with open(filepath_djrepo, 'w', encoding='utf-8') as handle:
             json.dump(data, handle)
             handle.flush()
 
-        filename_metadata = shutil.make_archive('tempmetadata', 'gztar', root_dir=tmpdir, base_dir='.')
+        filename_metadata = shutil.make_archive('tempmetadata', 'gztar', root_dir=tmp_path, base_dir='.')
         shutil.move(pathlib.Path.cwd() / filename_metadata, filepath_metadata)
 
     def _run_monkeypatched_install_pseudo_dojo(options=None, raises=None):
@@ -134,7 +134,7 @@ def test_install_family_folder(run_cli_command, filepath_pseudos):
     label = 'family_test'
     description = 'description'
     dirpath = filepath_pseudos()
-    options = ['-D', description, dirpath, label]
+    options = ['-D', description, str(dirpath), label]
 
     result = run_cli_command(cmd_install_family, options)
     assert f'installed `{label}`' in result.output
@@ -269,7 +269,7 @@ def test_install_pseudo_dojo_monkeypatched(run_monkeypatched_install_pseudo_dojo
     assert family.label == label
 
 
-@pytest.mark.usefixtures('clear_db', 'chtmpdir')
+@pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
 def test_install_sssp_download_only(run_monkeypatched_install_sssp):
     """Test the ``aiida-pseudo install sssp`` command with the ``--download-only`` option."""
     options = ['--download-only']
@@ -279,7 +279,7 @@ def test_install_sssp_download_only(run_monkeypatched_install_sssp):
     assert 'written to the current directory.' in result.output
 
 
-@pytest.mark.usefixtures('clear_db', 'chtmpdir')
+@pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
 def test_install_sssp_download_only_exists(run_monkeypatched_install_sssp, get_pseudo_family):
     """Test the ``aiida-pseudo install sssp`` command with the ``--download-only`` option.
 
@@ -300,7 +300,7 @@ def test_install_sssp_download_only_exists(run_monkeypatched_install_sssp, get_p
     assert 'written to the current directory.' in result.output
 
 
-@pytest.mark.usefixtures('clear_db', 'chtmpdir')
+@pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
 def test_install_pseudo_dojo_download_only(run_monkeypatched_install_pseudo_dojo):
     """Test the ``aiida-pseudo install pseudo-dojo`` command with the ``--download-only`` option."""
     options = ['--download-only']
@@ -310,7 +310,7 @@ def test_install_pseudo_dojo_download_only(run_monkeypatched_install_pseudo_dojo
     assert 'written to the current directory.' in result.output
 
 
-@pytest.mark.usefixtures('clear_db', 'chtmpdir')
+@pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
 def test_install_pseudo_dojo_download_only_exists(run_monkeypatched_install_pseudo_dojo, get_pseudo_family):
     """Test the ``aiida-pseudo install pseudo_dojo`` command with the ``--download-only`` option.
 

tests/cli/test_utils.py

@@ -25,19 +25,19 @@ def test_create_family_from_archive(get_pseudo_archive, fmt):
 
 
 @pytest.mark.usefixtures('clear_db')
-def test_create_family_from_archive_incorrect_filetype(tmpdir):
+def test_create_family_from_archive_incorrect_filetype(tmp_path):
     """Test the `create_family_from_archive` utility function for incorrect archive filetype."""
     with pytest.raises(OSError, match=r'failed to unpack the archive.*'):
-        create_family_from_archive(PseudoPotentialFamily, 'label', str(tmpdir))
+        create_family_from_archive(PseudoPotentialFamily, 'label', tmp_path)
 
 
 @pytest.mark.usefixtures('clear_db')
-def test_create_family_from_archive_incorrect_format(tmpdir):
+def test_create_family_from_archive_incorrect_format(tmp_path):
     """Test the `create_family_from_archive` utility function for invalid archive content."""
     with tempfile.NamedTemporaryFile(suffix='.tar.gz') as filepath_archive:
 
         with tarfile.open(filepath_archive.name, 'w:gz') as tar:
-            tar.add(str(tmpdir), arcname='.')
+            tar.add(tmp_path, arcname='.')
 
         with pytest.raises(OSError, match=r'failed to parse pseudos from.*'):
             create_family_from_archive(PseudoPotentialFamily, 'label', filepath_archive.name)