CLI: separate established families from non-established ones

aiida_pseudo/cli/family.py

@@ -8,7 +8,7 @@
 from aiida.cmdline.utils import decorators, echo
 
 from ..groups.mixins import RecommendedCutoffMixin
-from .params import arguments, options
+from .params import arguments, options, types
 from .root import cmd_root
 
 
@@ -57,7 +57,9 @@ def cmd_family_cutoffs():
 
 
 @cmd_family_cutoffs.command('set')
-@arguments.PSEUDO_POTENTIAL_FAMILY()
+@arguments.PSEUDO_POTENTIAL_FAMILY(
+    type=types.PseudoPotentialFamilyParam(exclude=('pseudo.family.sssp', 'pseudo.family.pseudo_dojo'))
+)
 @click.argument('cutoffs', type=click.File(mode='rb'))
 @options.STRINGENCY(required=True)
 @options.UNIT()
@@ -86,8 +88,15 @@ def cmd_family_cutoffs_set(family, cutoffs, stringency, unit):  # noqa: D301
     except ValueError as exception:
         raise click.BadParameter(f'`{cutoffs.name}` contains invalid JSON: {exception}', param_hint='CUTOFFS')
 
+    cutoffs_dict = dict()
+    for element, values in data.items():
+        try:
+            cutoffs_dict[element] = {'cutoff_wfc': values['cutoff_wfc'], 'cutoff_rho': values['cutoff_rho']}
+        except KeyError as exception:
+            raise click.BadParameter(f'`{cutoffs.name}` is missing cutoffs for element: {element}') from exception
+
     try:
-        family.set_cutoffs(data, stringency, unit=unit)
+        family.set_cutoffs(cutoffs_dict, stringency, unit=unit)
     except ValueError as exception:
         raise click.BadParameter(f'`{cutoffs.name}` contains invalid cutoffs: {exception}', param_hint='CUTOFFS')
 

aiida_pseudo/cli/install.py

@@ -4,6 +4,7 @@
 import pathlib
 import shutil
 import tempfile
+import tarfile
 
 import click
 import requests
@@ -167,54 +168,28 @@ def download_pseudo_dojo(
 @options.FUNCTIONAL(type=click.Choice(['PBE', 'PBEsol']), default='PBE', show_default=True)
 @options.PROTOCOL(type=click.Choice(['efficiency', 'precision']), default='efficiency', show_default=True)
 @options.DOWNLOAD_ONLY()
+@options.FROM_DOWNLOAD()
 @options.TRACEBACK()
 @decorators.with_dbenv()
-def cmd_install_sssp(version, functional, protocol, download_only, traceback):
+def cmd_install_sssp(version, functional, protocol, download_only, from_download, traceback):
     """Install an SSSP configuration.
 
     The SSSP configuration will be automatically downloaded from the Materials Cloud Archive entry to create a new
     `SsspFamily`.
     """
-    # pylint: disable=too-many-locals
+    # pylint: disable=too-many-locals, too-many-statements
     from aiida.common.files import md5_file
     from aiida.orm import Group, QueryBuilder
 
     from aiida_pseudo import __version__
     from aiida_pseudo.groups.family import SsspFamily
     from .utils import attempt, create_family_from_archive
 
-    configuration = SsspConfiguration(version, functional, protocol)
-    label = SsspFamily.format_configuration_label(configuration)
-    description = f'SSSP v{version} {functional} {protocol} installed with aiida-pseudo v{__version__}'
-
-    if configuration not in SsspFamily.valid_configurations:
-        echo.echo_critical(f'{version} {functional} {protocol} is not a valid SSSP configuration')
-
-    if not download_only and QueryBuilder().append(SsspFamily, filters={'label': label}).first():
-        echo.echo_critical(f'{SsspFamily.__name__}<{label}> is already installed')
-
-    with tempfile.TemporaryDirectory() as dirpath:
-
-        dirpath = pathlib.Path(dirpath)
-        filepath_archive = dirpath / 'archive.tar.gz'
-        filepath_metadata = dirpath / 'metadata.json'
-
-        download_sssp(configuration, filepath_archive, filepath_metadata, traceback)
+    def install_sssp(filepath_archive, filepath_metadata, label, description):
 
         description += f'\nArchive pseudos md5: {md5_file(filepath_archive)}'
         description += f'\nPseudo metadata md5: {md5_file(filepath_metadata)}'
 
-        if download_only:
-            for filepath in [filepath_archive, filepath_metadata]:
-                filepath_target = pathlib.Path.cwd() / filepath.name
-                if filepath_target.exists():
-                    echo.echo_warning(f'the file `{filepath_target}` already exists, skipping.')
-                else:
-                    # Cannot use ``pathlib.Path.rename`` because this will fail if it moves across file systems.
-                    shutil.move(filepath, filepath_target)
-                    echo.echo_success(f'`{filepath_target.name}` written to the current directory.')
-            return
-
         with open(filepath_metadata, 'rb') as handle:
             handle.seek(0)
             metadata = json.load(handle)
@@ -237,6 +212,63 @@ def cmd_install_sssp(version, functional, protocol, download_only, traceback):
 
         echo.echo_success(f'installed `{label}` containing {family.count()} pseudopotentials')
 
+    if download_only and from_download is not None:
+        raise click.BadParameter(
+            'cannot specify both `--download-only` and `--from-download`.',
+            param_hint="'--download-only' / '--from-download'"
+        )
+
+    configuration = SsspConfiguration(version, functional, protocol)
+
+    if configuration not in SsspFamily.valid_configurations:
+        echo.echo_critical(f'{version} {functional} {protocol} is not a valid SSSP configuration')
+
+    with tempfile.TemporaryDirectory() as dirpath:
+
+        dirpath = pathlib.Path(dirpath)
+
+        filepath_archive = dirpath / 'archive.tar.gz'
+        filepath_metadata = dirpath / 'metadata.json'
+
+        if from_download is not None:
+
+            tarball_path = pathlib.Path(from_download).absolute()
+            with tarfile.open(tarball_path, 'r') as handle:
+                handle.extractall(dirpath)
+
+            filepath_configuration = dirpath / 'configuration.json'
+
+            with filepath_configuration.open('r') as handle:
+                configuration = SsspConfiguration(**json.load(handle))
+        else:
+            download_sssp(configuration, filepath_archive, filepath_metadata, traceback)
+
+        label = SsspFamily.format_configuration_label(configuration)
+        description = (
+            f'SSSP v{configuration.version} {configuration.functional} {configuration.protocol} '
+            f'installed with aiida-pseudo v{__version__}'
+        )
+        if not download_only and QueryBuilder().append(SsspFamily, filters={'label': label}).first():
+            echo.echo_critical(f'{SsspFamily.__name__}<{label}> is already installed')
+
+        if download_only:
+            filepath_configuration = dirpath / 'configuration.json'
+
+            with filepath_configuration.open('w') as handle:
+                handle.write(json.dumps(configuration._asdict()))
+
+            tarball_path = pathlib.Path.cwd() / f'{label}.aiida_pseudo'.replace('/', '_')
+
+            if tarball_path.exists():
+                echo.echo_critical(f'the file `{tarball_path}` already exists.')
+
+            with tarfile.open(tarball_path, 'w') as tarball_file:
+                for filepath in [filepath_configuration, filepath_metadata, filepath_archive]:
+                    tarball_file.add(filepath, filepath.name)
+            return
+
+        install_sssp(filepath_archive, filepath_metadata, label, description)
+
 
 @cmd_install.command('pseudo-dojo')
 @options.VERSION(type=click.Choice(['0.4', '1.0']), default='0.4', show_default=True)
@@ -246,10 +278,12 @@ def cmd_install_sssp(version, functional, protocol, download_only, traceback):
 @options.PSEUDO_FORMAT(type=click.Choice(['psp8', 'upf', 'psml', 'jthxml']), default='psp8', show_default=True)
 @options.DEFAULT_STRINGENCY(type=click.Choice(['low', 'normal', 'high']), default='normal', show_default=True)
 @options.DOWNLOAD_ONLY()
+@options.FROM_DOWNLOAD()
 @options.TRACEBACK()
 @decorators.with_dbenv()
 def cmd_install_pseudo_dojo(
-    version, functional, relativistic, protocol, pseudo_format, default_stringency, download_only, traceback
+    version, functional, relativistic, protocol, pseudo_format, default_stringency, download_only, from_download,
+    traceback
 ):
     """Install a PseudoDojo configuration.
 
@@ -281,6 +315,12 @@ def cmd_install_pseudo_dojo(
     )
     # yapf: enable
 
+    if download_only and from_download is not None:
+        raise click.BadParameter(
+            'cannot specify both `--download-only` and `--from-download`.',
+            param_hint="'--download-only' / '--from-download'"
+        )
+
     try:
         pseudo_type = pseudo_type_mapping[pseudo_format]
     except KeyError:
@@ -298,11 +338,16 @@ def cmd_install_pseudo_dojo(
 
     with tempfile.TemporaryDirectory() as dirpath:
 
-        dirpath = pathlib.Path(dirpath)
+        if from_download is not None:
+            dirpath = pathlib.Path(from_download).absolute()
+        else:
+            dirpath = pathlib.Path(dirpath)
+
         filepath_archive = dirpath / 'archive.tgz'
         filepath_metadata = dirpath / 'metadata.tgz'
 
-        download_pseudo_dojo(configuration, filepath_archive, filepath_metadata, traceback)
+        if from_download is None:
+            download_pseudo_dojo(configuration, filepath_archive, filepath_metadata, traceback)
 
         description += f'\nArchive pseudos md5: {md5_file(filepath_archive)}'
         description += f'\nPseudo metadata md5: {md5_file(filepath_metadata)}'

aiida_pseudo/cli/params/options.py

@@ -103,3 +103,12 @@
         'pseudopotential family.'
     )
 )
+
+FROM_DOWNLOAD = OverridableOption(
+    '--from-download',
+    type=click.STRING,
+    required=False,
+    default=None,
+    show_default=False,
+    help='Install the pseudpotential family from the archive and metadata downloaded with the `--download-only` option.'
+)

aiida_pseudo/cli/params/types.py

@@ -57,6 +57,27 @@ class PseudoPotentialFamilyParam(GroupParamType):
 
     name = 'pseudo_family'
 
+    def __init__(self, exclude: typing.Optional[typing.List[str]] = None, **kwargs):
+        """Construct the parameter.
+
+        :param exclude: an optional list of values that should be considered invalid and will raise ``BadParameter``.
+        """
+        super().__init__(**kwargs)
+        self.exclude = exclude
+
+    def convert(self, value, param, ctx):
+        """Convert the entry point name to the corresponding class.
+
+        :param value: entry point name that should correspond to subclass of `PseudoPotentialFamily` group plugin
+        :return: the `PseudoPotentialFamily` subclass
+        :raises: `click.BadParameter` if the entry point cannot be loaded or is not subclass of `PseudoPotentialFamily`
+        """
+        family = super().convert(value, param, ctx)
+
+        if self.exclude and family.type_string in self.exclude:
+            raise click.BadParameter(f'Cannot modify cutoffs for established family `{family}`.')
+        return family
+
 
 class PseudoPotentialFamilyTypeParam(click.ParamType):
     """Parameter type for `click` commands to define a subclass of `PseudoPotentialFamily`."""

docs/source/_static/aiida-pseudo-custom.css

@@ -0,0 +1,3 @@
+.bigfont {
+    font-size: 140%;
+}

docs/source/conf.py

@@ -31,7 +31,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx_copybutton', 'autoapi.extension', 'sphinx_click']
+extensions = ['sphinx_copybutton', 'autoapi.extension', 'sphinx_click', 'sphinx.ext.intersphinx']
 
 # Settings for the `sphinx_copybutton` extension
 copybutton_selector = 'div:not(.no-copy)>div.highlight pre'
@@ -42,6 +42,11 @@
 autoapi_dirs = ['../../aiida_pseudo']
 autoapi_ignore = ['*cli*']
 
+# Settings for the `sphinx.ext.intersphinx` extension
+intersphinx_mapping = {
+    'aiida': ('http://aiida_core.readthedocs.io/en/latest/', None),
+}
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -57,16 +62,21 @@
 #
 html_theme = 'sphinx_book_theme'
 html_static_path = ['_static']
-html_css_files = ['aiida-custom.css']
+html_css_files = [
+    'aiida-custom.css',
+    'aiida-pseudo-custom.css'
+]
 html_theme_options = {
     'home_page_in_toc': True,
     'repository_url': 'https://github.com/aiidateam/aiida-pseudo',
     'repository_branch': 'master',
     'use_repository_button': True,
     'use_issues_button': True,
+    'use_fullscreen_button': False,
     'path_to_docs': 'docs',
     'use_edit_page_button': True,
-    'extra_navbar': ''
+    'extra_navbar': '',
+    'extra_navbar': '<p>Made possible by the support of <a href="http://nccr-marvel.ch/" target="_blank"> NCCR MARVEL</a>, <a href="http://www.max-centre.eu/" target="_blank"> MaX CoE</a> and the <a href="https://www.materialscloud.org/swissuniversities" target="_blank"> swissuniversities P-5 project</a>.</p>'
 }
 html_domain_indices = True
 html_logo = '_static/logo.png'