From dac10c01fc387517717c92f0f5242f97e81e4d41 Mon Sep 17 00:00:00 2001
From: Marnik Bercx <mbercx@gmail.com>
Date: Sun, 3 Sep 2023 22:36:37 +0200
Subject: [PATCH] Update code after rebase

---
 docs/source/howto.rst                  |   9 +-
 docs/source/troubleshooting.rst        |  22 +-
 src/aiida_pseudo/cli/install.py        | 375 ++++++++++++++++---------
 src/aiida_pseudo/cli/params/options.py |  10 +
 tests/cli/test_install.py              |  49 +++-
 tests/groups/family/test_pseudo.py     |   2 +-
 6 files changed, 325 insertions(+), 142 deletions(-)

diff --git a/docs/source/howto.rst b/docs/source/howto.rst
index fa16e7d..5cf93c9 100644
--- a/docs/source/howto.rst
+++ b/docs/source/howto.rst
@@ -28,12 +28,16 @@ Similar to the `SSSP`_ pseudopotential family, the options can be used to set ve
 Moreover, the format of the pseudopotentials can be specified, as well as the default stringency.
 Use ``aiida-pseudo install pseudo-dojo --help`` for more information.
 
+.. note::
+
+    In case you are unable to use these automated commands because of connection issues, please consult the :ref:`troubleshooting section <troubleshooting:automated-fail>`.
+
 .. _how-to:install_archive:
 
 Installing from archive or folder
 =================================
 
-In case the automated install commands fail, or the pseudopotential family you want to use is not supported, you can install the pseudopotential family manually with the following command:
+In case the pseudopotential family you want to use is not supported, you can install the pseudopotential family manually with the following command:
 
 .. code-block:: console
 
@@ -53,7 +57,7 @@ If this fails, you can specify the format manually with the ``--archive-format/-
 
     $ aiida-pseudo install family <ARCHIVE> <LABEL> -f gztar
 
-The valid archive formats are those [defined by the ``shutil.unpack_archive`` function](https://docs.python.org/3/library/shutil.html#shutil.unpack_archive) of the standard Python library.
+The valid archive formats are those defined by the `shutil.unpack_archive <https://docs.python.org/3/library/shutil.html#shutil.unpack_archive>`_ function of the standard Python library.
 
 Pseudopotential format
 ----------------------
@@ -93,6 +97,7 @@ The available pseudopotential family classes can be listed with the command:
 .. important::
 
     The ``pseudo.family.sssp`` and ``pseudo.family.pseudo_dojo`` family types are blacklisted since they have their own :ref:`dedicated install commands <how-to:install_automated>` in ``aiida-pseudo install sssp`` and ``aiida-pseudo install pseudo-dojo``, respectively.
+    In case you are unable to use these commands because of connection issues, please consult the :ref:`troubleshooting section <troubleshooting:automated-fail>`.
 
 Adding recommended cutoffs
 --------------------------
diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index da19464..20ebf54 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -5,9 +5,27 @@
 Troubleshooting
 ###############
 
+.. _troubleshooting:automated-fail:
+
 The automated install commands fail
 ===================================
 
 These failures are often due to unstable internet connections causing the download of the pseudopotential archive from the web to fail.
-In this case, it is possible to install the family manually from an archive that is already available on the local file system.
-You can read more on this in the :ref:`how-to section <how-to:install_archive>`.
+In this case, it is possible to download an ``.aiida_pseudo`` archive of the established family, transfer them to the machine where the pseudopotentials need to be installed and install directly from the archive.
+To download the archive, use the ``--download-only`` option:
+
+.. code-block:: console
+
+    $ aiida-pseudo install sssp --download-only
+    Report: downloading patch versions information...  [OK]
+    Report: downloading selected pseudopotentials archive...  [OK]
+    Report: downloading selected pseudopotentials metadata...  [OK]
+    Success: Pseudopotential archive written to: SSSP_1.1_PBE_efficiency.aiida_pseudo
+
+The downloaded archive can be installed through the ``--from-download`` option of the corresponding install command:
+
+.. code-block:: console
+
+    $ aiida-pseudo install sssp --from-download SSSP_1.1_PBE_efficiency.aiida_pseudo
+    Report: unpacking archive and parsing pseudos...  [OK]
+    Success: installed `SSSP/1.1/PBE/efficiency` containing 85 pseudopotentials.
diff --git a/src/aiida_pseudo/cli/install.py b/src/aiida_pseudo/cli/install.py
index 635c255..68d7fa2 100644
--- a/src/aiida_pseudo/cli/install.py
+++ b/src/aiida_pseudo/cli/install.py
@@ -2,8 +2,8 @@
 """Command to install a pseudo potential family."""
 import json
 import pathlib
-import shutil
 import sys
+import tarfile
 import tempfile
 import typing as t
 
@@ -17,7 +17,8 @@
 from .root import cmd_root
 
 if t.TYPE_CHECKING:
-    from aiida_pseudo.groups.family import SsspConfiguration
+    from aiida_pseudo.data.pseudo import PseudoPotentialData
+    from aiida_pseudo.groups.family import PseudoDojoConfiguration, PseudoDojoFamily, SsspConfiguration
 
 
 @cmd_root.group('install')
@@ -148,40 +149,48 @@ def download_sssp(
     return patch_version
 
 
-def download_pseudo_dojo(
-    configuration: 'SsspConfiguration',
+def install_sssp(
     filepath_archive: pathlib.Path,
     filepath_metadata: pathlib.Path,
+    label: str,
+    description: str = '',
     traceback: bool = False
 ) -> None:
-    """Download the pseudopotential archive and metadata for a PseudoDojo configuration to a path on disk.
+    """Install the ``SsspFamily`` and set the recommended cutoffs.
 
-    :param configuration: the PseudoDojo configuration to download.
-    :param filepath_archive: absolute filepath to write the pseudopotential archive to.
-    :param filepath_metadata: absolute filepath to write the metadata archive to.
+    :param filepath_archive: path to the pseudopotential archive.
+    :param filepath_metadata: path to the metadata file.
+    :param label: label of the pseudopotential family group.
+    :param description: description of the pseudopotential family group.
     :param traceback: boolean, if true, print the traceback when an exception occurs.
     """
-    from aiida_pseudo.groups.family import PseudoDojoFamily
+    # pylint: disable=too-many-locals
+    from aiida.orm import Group
 
-    from .utils import attempt
+    from ..groups.family.sssp import SsspFamily
+    from .utils import attempt, create_family_from_archive
 
-    label = PseudoDojoFamily.format_configuration_label(configuration)
-    url_archive = PseudoDojoFamily.get_url_archive(label)
-    url_metadata = PseudoDojoFamily.get_url_metadata(label)
+    with open(filepath_metadata, 'rb') as handle:
+        handle.seek(0)
+        metadata = json.load(handle)
 
-    with attempt('downloading selected pseudopotentials archive... ', include_traceback=traceback):
-        response = requests.get(url_archive, timeout=30)
-        response.raise_for_status()
-        with open(filepath_archive, 'wb') as handle:
-            handle.write(response.content)
-            handle.flush()
+    with attempt('unpacking archive and parsing pseudos... ', include_traceback=traceback):
+        family = create_family_from_archive(SsspFamily, label, filepath_archive)
 
-    with attempt('downloading selected pseudopotentials metadata archive... ', include_traceback=traceback):
-        response = requests.get(url_metadata, timeout=30)
-        response.raise_for_status()
-        with open(filepath_metadata, 'wb') as handle:
-            handle.write(response.content)
-            handle.flush()
+    cutoffs = {}
+
+    for element, values in metadata.items():
+        if family.get_pseudo(element).md5 != values['md5']:
+            Group.collection.delete(family.pk)
+            msg = f"md5 of pseudo for element {element} does not match that of the metadata {values['md5']}"
+            echo.echo_critical(msg)
+
+        cutoffs[element] = {'cutoff_wfc': values['cutoff_wfc'], 'cutoff_rho': values['cutoff_rho']}
+
+    family.description = description
+    family.set_cutoffs(cutoffs, 'normal', unit='Ry')
+
+    echo.echo_success(f'installed `{label}` containing {family.count()} pseudopotentials.')
 
 
 @cmd_install.command('sssp')
@@ -189,77 +198,197 @@ 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.orm import QueryBuilder
 
     from aiida_pseudo import __version__
-    from aiida_pseudo.groups.family import SsspConfiguration, SsspFamily
 
-    from .utils import attempt, create_family_from_archive
+    from ..groups.family.sssp import SsspConfiguration, SsspFamily
+
+    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)
-    label = SsspFamily.format_configuration_label(configuration)
 
     if configuration not in SsspFamily.valid_configurations:
-        echo.echo_critical(f'{configuration} is not a valid configuration.')
-
-    if not download_only and QueryBuilder().append(SsspFamily, filters={'label': label}).first():
-        echo.echo_report(f'{SsspFamily.__name__}<{label}> is already installed')
-        sys.exit(1)
+        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'
 
-        patch_version = download_sssp(configuration, filepath_archive, filepath_metadata, traceback)
+        if from_download is not None:
 
-        description = f'SSSP v{patch_version} {functional} {protocol} installed with aiida-pseudo v{__version__}'
-        description += f'\nArchive pseudos md5: {md5_file(filepath_archive)}'
-        description += f'\nPseudo metadata md5: {md5_file(filepath_metadata)}'
+            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)
+
+        if not download_only and QueryBuilder().append(SsspFamily, filters={'label': label}).first():
+            echo.echo_report(f'{SsspFamily.__name__}<{label}> is already installed')
+            sys.exit(1)
 
         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.')
+            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)
+            echo.echo_success(f'Pseudopotential archive written to: {tarball_path.name}')
             return
 
-        with open(filepath_metadata, 'rb') as handle:
-            handle.seek(0)
-            metadata = json.load(handle)
+        description = (
+            f'SSSP v{configuration.version} {configuration.functional} {configuration.protocol} '
+            f'installed with aiida-pseudo v{__version__}'
+        )
+        description += f'\nArchive pseudos md5: {md5_file(filepath_archive)}'
+        description += f'\nPseudo metadata md5: {md5_file(filepath_metadata)}'
 
-        with attempt('unpacking archive and parsing pseudos... ', include_traceback=traceback):
-            family = create_family_from_archive(SsspFamily, label, filepath_archive)
+        install_sssp(filepath_archive, filepath_metadata, label, description, traceback)
+
+
+def download_pseudo_dojo(
+    configuration: 'PseudoDojoConfiguration',
+    filepath_archive: pathlib.Path,
+    filepath_metadata: pathlib.Path,
+    traceback: bool = False
+) -> None:
+    """Download the pseudopotential archive and metadata for a PseudoDojo configuration to a path on disk.
+
+    :param configuration: the PseudoDojo configuration to download.
+    :param filepath_archive: absolute filepath to write the pseudopotential archive to.
+    :param filepath_metadata: absolute filepath to write the metadata archive to.
+    :param traceback: boolean, if true, print the traceback when an exception occurs.
+    """
+    from ..groups.family.pseudo_dojo import PseudoDojoFamily
+    from .utils import attempt
+
+    label = PseudoDojoFamily.format_configuration_label(configuration)
+    url_archive = PseudoDojoFamily.get_url_archive(label)
+    url_metadata = PseudoDojoFamily.get_url_metadata(label)
+
+    with attempt('downloading selected pseudopotentials archive... ', include_traceback=traceback):
+        response = requests.get(url_archive, timeout=30)
+        response.raise_for_status()
+        with open(filepath_archive, 'wb') as handle:
+            handle.write(response.content)
+            handle.flush()
+
+    with attempt('downloading selected pseudopotentials metadata archive... ', include_traceback=traceback):
+        response = requests.get(url_metadata, timeout=30)
+        response.raise_for_status()
+        with open(filepath_metadata, 'wb') as handle:
+            handle.write(response.content)
+            handle.flush()
 
-        cutoffs = {}
 
-        for element, values in metadata.items():
-            if family.get_pseudo(element).md5 != values['md5']:
-                Group.collection.delete(family.pk)
-                msg = f"md5 of pseudo for element {element} does not match that of the metadata {values['md5']}"
-                echo.echo_critical(msg)
+def install_pseudo_dojo(
+    configuration: 'PseudoDojoConfiguration',
+    filepath_archive: pathlib.Path,
+    filepath_metadata: pathlib.Path,
+    pseudo_type: 'PseudoPotentialData',
+    label: str,
+    description: str = '',
+    traceback: bool = False
+) -> 'PseudoDojoFamily':
+    """Install the ``PseudoDojoFamily`` and set the recommended cutoffs.
+
+    :param filepath_archive: path to the pseudopotential archive.
+    :param filepath_metadata: path to the metadata file.
+    :param label: label of the pseudopotential family group.
+    :pseudo_type: type of the pseudopotentials (psp8, upf, ...).
+    :param description: description of the pseudopotential family group.
+    :param traceback: boolean, if true, print the traceback when an exception occurs.
+    """
+    # pylint: disable=too-many-locals
+    from aiida.orm import Group
+
+    from ..groups.family.pseudo_dojo import PseudoDojoConfiguration, PseudoDojoFamily
+    from .utils import attempt, create_family_from_archive
+
+    with attempt('unpacking archive and parsing pseudos... ', include_traceback=traceback):
+        family = create_family_from_archive(PseudoDojoFamily, label, filepath_archive, pseudo_type=pseudo_type)
+
+    with attempt('unpacking metadata archive and parsing metadata...', include_traceback=traceback):
+        md5s, cutoffs = PseudoDojoFamily.parse_djrepos_from_archive(filepath_metadata, pseudo_type=pseudo_type)
+
+    for element, md5 in md5s.items():
+        if family.get_pseudo(element).md5 != md5:
+            Group.collection.delete(family.pk)
+            msg = f'md5 of pseudo for element {element} does not match that of the metadata {md5}'
+            echo.echo_critical(msg)
+
+    # yapf: disable
+    paw_configurations = (
+        PseudoDojoConfiguration('1.0', 'PBE', 'SR', 'standard', 'jthxml'),
+        PseudoDojoConfiguration('1.0', 'PBE', 'SR', 'stringent', 'jthxml'),
+        PseudoDojoConfiguration('1.0', 'LDA', 'SR', 'standard', 'jthxml'),
+        PseudoDojoConfiguration('1.0', 'LDA', 'SR', 'stringent', 'jthxml')
+    )
+    # yapf: enable
+
+    # The PAW configurations have missing cutoffs for the Lanthanides, which have ben replaced with a placeholder
+    # value of `-1`. We replace these with the 1.5 * the maximum cutoff from the same stringency so that these
+    # potentials are still usable, but this should be taken as a _rough_ approximation.
+    # We check only the `cutoff_wfc` because `cutoff_rho` is not provided by PseudoDojo and is therefore
+    # locally calculated in `PseudoDojoFamily.parse_djrepos_from_archive` as `2.0 * cutoff_wfc` for PAW.
+    if configuration in paw_configurations:
+        adjusted_cutoffs = {}
+        for stringency, str_cutoffs in cutoffs.items():
+            adjusted_cutoffs[stringency] = []
+            max_cutoff_wfc = max(cutoffs['cutoff_wfc'] for cutoffs in str_cutoffs.values())
+            filler_cutoff_wfc = max_cutoff_wfc * 1.5
+            for element, cutoff in str_cutoffs.items():
+                if cutoff['cutoff_wfc'] <= 0:
+                    cutoffs[stringency][element]['cutoff_wfc'] = filler_cutoff_wfc
+                    cutoffs[stringency][element]['cutoff_rho'] = 2.0 * filler_cutoff_wfc
+                    adjusted_cutoffs[stringency].append(element)
+
+        for stringency, elements in adjusted_cutoffs.items():
+            msg = f'stringency `{stringency}` has missing recommended cutoffs for elements ' \
+                f'{", ".join(elements)}: as a substitute, 1.5 * the maximum cutoff of the stringency ' \
+                'was set for these elements. USE WITH CAUTION!'
+            echo.echo_warning(msg)
 
-            cutoffs[element] = {'cutoff_wfc': values['cutoff_wfc'], 'cutoff_rho': values['cutoff_rho']}
+    family.description = description
+    for stringency, cutoff_values in cutoffs.items():
+        family.set_cutoffs(cutoff_values, stringency, unit='Eh')
 
-        family.description = description
-        family.set_cutoffs(cutoffs, 'normal', unit='Ry')
+    echo.echo_success(f'installed `{label}` containing {family.count()} pseudopotentials.')
 
-        echo.echo_success(f'installed `{label}` containing {family.count()} pseudopotentials.')
+    return family
 
 
 @cmd_install.command('pseudo-dojo')
@@ -270,10 +399,12 @@ 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.
 
@@ -282,13 +413,17 @@ def cmd_install_pseudo_dojo(
     """
     # pylint: disable=too-many-locals,too-many-arguments,too-many-branches,too-many-statements
     from aiida.common.files import md5_file
-    from aiida.orm import Group, QueryBuilder
+    from aiida.orm import QueryBuilder
 
     from aiida_pseudo import __version__
     from aiida_pseudo.data.pseudo import JthXmlData, PsmlData, Psp8Data, UpfData
-    from aiida_pseudo.groups.family import PseudoDojoConfiguration, PseudoDojoFamily
+    from aiida_pseudo.groups.family.pseudo_dojo import PseudoDojoConfiguration, PseudoDojoFamily
 
-    from .utils import attempt, create_family_from_archive
+    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'"
+        )
 
     pseudo_type_mapping = {
         'jthxml': JthXmlData,
@@ -297,15 +432,6 @@ def cmd_install_pseudo_dojo(
         'upf': UpfData,
     }
 
-    # yapf: disable
-    paw_configurations = (
-        PseudoDojoConfiguration('1.0', 'PBE', 'SR', 'standard', 'jthxml'),
-        PseudoDojoConfiguration('1.0', 'PBE', 'SR', 'stringent', 'jthxml'),
-        PseudoDojoConfiguration('1.0', 'LDA', 'SR', 'standard', 'jthxml'),
-        PseudoDojoConfiguration('1.0', 'LDA', 'SR', 'stringent', 'jthxml')
-    )
-    # yapf: enable
-
     try:
         pseudo_type = pseudo_type_mapping[pseudo_format]
     except KeyError:
@@ -313,75 +439,58 @@ def cmd_install_pseudo_dojo(
 
     configuration = PseudoDojoConfiguration(version, functional, relativistic, protocol, pseudo_format)
     label = PseudoDojoFamily.format_configuration_label(configuration)
-    description = f'{configuration} installed with aiida-pseudo v{__version__}'
 
     if configuration not in PseudoDojoFamily.valid_configurations:
         echo.echo_critical(f'{configuration} is not a valid configuration')
 
-    if not download_only and QueryBuilder().append(PseudoDojoFamily, filters={'label': label}).first():
-        echo.echo_report(f'{PseudoDojoFamily.__name__}<{label}> is already installed.')
-        sys.exit(1)
-
     with tempfile.TemporaryDirectory() as dirpath:
 
         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 not None:
 
-        description += f'\nArchive pseudos md5: {md5_file(filepath_archive)}'
-        description += f'\nPseudo metadata md5: {md5_file(filepath_metadata)}'
+            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 = PseudoDojoConfiguration(**json.load(handle))
+                pseudo_type = pseudo_type_mapping[configuration.pseudo_format]
+        else:
+            download_pseudo_dojo(configuration, filepath_archive, filepath_metadata, traceback)
+
+        label = PseudoDojoFamily.format_configuration_label(configuration)
+
+        if not download_only and QueryBuilder().append(PseudoDojoFamily, filters={'label': label}).first():
+            echo.echo_report(f'{PseudoDojoFamily.__name__}<{label}> is already installed')
+            sys.exit(1)
 
         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.')
+            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)
+            echo.echo_success(f'Pseudopotential archive written to: {tarball_path.name}')
             return
 
-        with attempt('unpacking archive and parsing pseudos... ', include_traceback=traceback):
-            family = create_family_from_archive(PseudoDojoFamily, label, filepath_archive, pseudo_type=pseudo_type)
-
-        with attempt('unpacking metadata archive and parsing metadata...', include_traceback=traceback):
-            md5s, cutoffs = PseudoDojoFamily.parse_djrepos_from_archive(filepath_metadata, pseudo_type=pseudo_type)
-
-        for element, md5 in md5s.items():
-            if family.get_pseudo(element).md5 != md5:
-                Group.collection.delete(family.pk)
-                msg = f'md5 of pseudo for element {element} does not match that of the metadata {md5}'
-                echo.echo_critical(msg)
-
-        # The PAW configurations have missing cutoffs for the Lanthanides, which have ben replaced with a placeholder
-        # value of `-1`. We replace these with the 1.5 * the maximum cutoff from the same stringency so that these
-        # potentials are still usable, but this should be taken as a _rough_ approximation.
-        # We check only the `cutoff_wfc` because `cutoff_rho` is not provided by PseudoDojo and is therefore
-        # locally calculated in `PseudoDojoFamily.parse_djrepos_from_archive` as `2.0 * cutoff_wfc` for PAW.
-        if configuration in paw_configurations:
-            adjusted_cutoffs = {}
-            for stringency, str_cutoffs in cutoffs.items():
-                adjusted_cutoffs[stringency] = []
-                max_cutoff_wfc = max(cutoffs['cutoff_wfc'] for cutoffs in str_cutoffs.values())
-                filler_cutoff_wfc = max_cutoff_wfc * 1.5
-                for element, cutoff in str_cutoffs.items():
-                    if cutoff['cutoff_wfc'] <= 0:
-                        cutoffs[stringency][element]['cutoff_wfc'] = filler_cutoff_wfc
-                        cutoffs[stringency][element]['cutoff_rho'] = 2.0 * filler_cutoff_wfc
-                        adjusted_cutoffs[stringency].append(element)
-
-            for stringency, elements in adjusted_cutoffs.items():
-                msg = f'stringency `{stringency}` has missing recommended cutoffs for elements ' \
-                    f'{", ".join(elements)}: as a substitute, 1.5 * the maximum cutoff of the stringency ' \
-                    'was set for these elements. USE WITH CAUTION!'
-                echo.echo_warning(msg)
-
-        family.description = description
-        for stringency, cutoff_values in cutoffs.items():
-            family.set_cutoffs(cutoff_values, stringency, unit='Eh')
-        family.set_default_stringency(default_stringency)
-
-        echo.echo_success(f'installed `{label}` containing {family.count()} pseudopotentials.')
+        description = f'{configuration} installed with aiida-pseudo v{__version__}'
+        description += f'\nArchive pseudos md5: {md5_file(filepath_archive)}'
+        description += f'\nPseudo metadata md5: {md5_file(filepath_metadata)}'
+
+        install_pseudo_dojo(
+            configuration, filepath_archive, filepath_metadata, pseudo_type, label, description, traceback
+        ).set_default_stringency(default_stringency)
diff --git a/src/aiida_pseudo/cli/params/options.py b/src/aiida_pseudo/cli/params/options.py
index e45ce4b..f340a11 100644
--- a/src/aiida_pseudo/cli/params/options.py
+++ b/src/aiida_pseudo/cli/params/options.py
@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 """Reusable options for CLI commands."""
 import functools
+from pathlib import Path
 import shutil
 
 from aiida.cmdline.params import options as core_options
@@ -114,3 +115,12 @@
         'pseudopotential family.'
     )
 )
+
+FROM_DOWNLOAD = core_options.OverridableOption(
+    '--from-download',
+    type=click.Path(exists=True, dir_okay=False, path_type=Path),
+    required=False,
+    default=None,
+    show_default=False,
+    help='Install the pseudpotential family from the archive and metadata downloaded with the `--download-only` option.'
+)
diff --git a/tests/cli/test_install.py b/tests/cli/test_install.py
index 53397ba..e61a889 100644
--- a/tests/cli/test_install.py
+++ b/tests/cli/test_install.py
@@ -277,7 +277,7 @@ def test_install_sssp_download_only(run_monkeypatched_install_sssp):
     result = run_monkeypatched_install_sssp(options=options)
 
     assert SsspFamily.collection.count() == 0
-    assert 'written to the current directory.' in result.output
+    assert 'Success: Pseudopotential archive written to:' in result.output
 
 
 @pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
@@ -298,7 +298,25 @@ def test_install_sssp_download_only_exists(run_monkeypatched_install_sssp, get_p
     result = run_monkeypatched_install_sssp(options=options)
 
     assert SsspFamily.collection.count() == 1
-    assert 'written to the current directory.' in result.output
+    assert 'Success: Pseudopotential archive written to:' in result.output
+
+
+@pytest.mark.parametrize('configuration', SsspFamily.valid_configurations)
+@pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
+def test_install_sssp_from_download(run_monkeypatched_install_sssp, configuration):
+    """Test the ``aiida-pseudo install sssp`` command with the ``--from-download`` option."""
+    options = [
+        '--download-only', '-v', configuration.version, '-x', configuration.functional, '-p', configuration.protocol
+    ]
+    result = run_monkeypatched_install_sssp(options=options)
+
+    label = SsspFamily.format_configuration_label(configuration).replace('/', '_')
+    filepath = pathlib.Path.cwd() / f'{label}.aiida_pseudo'
+    options = ['--from-download', str(filepath)]
+
+    result = run_monkeypatched_install_sssp(options=options)
+    assert SsspFamily.collection.count() == 1
+    assert 'Success: installed `SSSP/' in result.output
 
 
 @pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
@@ -308,7 +326,7 @@ def test_install_pseudo_dojo_download_only(run_monkeypatched_install_pseudo_dojo
     result = run_monkeypatched_install_pseudo_dojo(options=options)
 
     assert PseudoDojoFamily.collection.count() == 0
-    assert 'written to the current directory.' in result.output
+    assert 'Success: Pseudopotential archive written to:' in result.output
 
 
 @pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
@@ -334,4 +352,27 @@ def test_install_pseudo_dojo_download_only_exists(run_monkeypatched_install_pseu
     result = run_monkeypatched_install_pseudo_dojo(options=options)
 
     assert PseudoDojoFamily.collection.count() == 1
-    assert 'written to the current directory.' in result.output
+    assert 'Success: Pseudopotential archive written to:' in result.output
+
+
+@pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
+def test_install_pseudo_dojo_from_download(run_monkeypatched_install_pseudo_dojo):
+    """Test the ``aiida-pseudo install pseudo-dojo`` command with the ``--from-download`` option."""
+    version = '1.0'
+    functional = 'LDA'
+    relativistic = 'SR'
+    protocol = 'stringent'
+    pseudo_format = 'jthxml'
+    configuration = PseudoDojoConfiguration(version, functional, relativistic, protocol, pseudo_format)
+    options = [
+        '--download-only', '-v', version, '-x', functional, '-r', relativistic, '-p', protocol, '-f', pseudo_format
+    ]
+    result = run_monkeypatched_install_pseudo_dojo(options=options)
+
+    label = PseudoDojoFamily.format_configuration_label(configuration).replace('/', '_')
+    filepath = pathlib.Path.cwd() / f'{label}.aiida_pseudo'
+    options = ['--from-download', str(filepath)]
+
+    result = run_monkeypatched_install_pseudo_dojo(options=options)
+    assert PseudoDojoFamily.collection.count() == 1
+    assert 'Success: installed `PseudoDojo' in result.output
diff --git a/tests/groups/family/test_pseudo.py b/tests/groups/family/test_pseudo.py
index bbf875f..f0e68df 100644
--- a/tests/groups/family/test_pseudo.py
+++ b/tests/groups/family/test_pseudo.py
@@ -153,7 +153,7 @@ def test_create_from_folder_duplicate_element(tmp_path, filepath_pseudos):
     dirpath = tmp_path / 'pseudos'
     shutil.copytree(filepath_pseudos(), dirpath)
 
-    (dirpath / 'Ar.UPF').touch()
+    (dirpath / 'Ar.upf_duplicate').touch()
 
     with pytest.raises(ValueError, match=r'directory `.*` contains pseudo potentials with duplicate elements'):
         PseudoPotentialFamily.create_from_folder(dirpath, 'label')