ORM: Move deprecation warnings from module level

The `aiida.orm.nodes.data.code.legacy` and `aiida.orm.nodes.data.upf`
modules contained deprecation warnings on the module level. Since these
were exposed directly on the `aiida.orm` level, these deprecations would
always show. This would even be the case if `warnings.showdeprecations`
would be disabled, because that acts on the profile by default, which is
not yet loaded at import time. Disabling the warnings globally would
work but this would not be intuitive for users.

The original reason for putting the warning on the module level is that
third-party code could rely on the module merely by importing the
classes without actually constructing it. This would make it possible
for some plugins to completely miss the deprecation warning.

At this point we decide to accept this risk in favor of reducing the
noise for the majority of users as these warnings are printed as soon as
anything from AiiDA is imported.

aiida/orm/nodes/data/code/legacy.py

@@ -20,13 +20,6 @@
 
 __all__ = ('Code',)
 
-warn_deprecation(
-    'The `Code` class is deprecated. To create an instance, use the `aiida.orm.nodes.data.code.installed.InstalledCode`'
-    ' or `aiida.orm.nodes.data.code.portable.PortableCode` for a "remote" or "local" code, respectively. If you are '
-    'using this class to compare type, e.g. in `isinstance`, use `aiida.orm.nodes.data.code.abstract.AbstractCode`.',
-    version=3
-)
-
 
 class Code(AbstractCode):
     """
@@ -50,6 +43,14 @@ class Code(AbstractCode):
     def __init__(self, remote_computer_exec=None, local_executable=None, input_plugin_name=None, files=None, **kwargs):
         super().__init__(**kwargs)
 
+        warn_deprecation(
+            'The `Code` class is deprecated. To create an instance, use the '
+            '`aiida.orm.nodes.data.code.installed.InstalledCode` or `aiida.orm.nodes.data.code.portable.PortableCode` '
+            'for a "remote" or "local" code, respectively. If you are using this class to compare type, e.g. in '
+            '`isinstance`, use `aiida.orm.nodes.data.code.abstract.AbstractCode`.',
+            version=3
+        )
+
         if remote_computer_exec and local_executable:
             raise ValueError('cannot set `remote_computer_exec` and `local_executable` at the same time')
 

aiida/orm/nodes/data/upf.py

@@ -19,11 +19,14 @@
 
 __all__ = ('UpfData',)
 
-warn_deprecation(
-    'This module is deprecated. See '
-    'https://aiida-pseudo.readthedocs.io/en/latest/howto.html#migrate-from-legacy-upfdata-from-aiida-core.',
-    version=3
-)
+
+def emit_deprecation():
+    warn_deprecation(
+        'The `aiida.orm.nodes.data.upf` module is deprecated. For details how to replace it, please see '
+        'https://aiida-pseudo.readthedocs.io/en/latest/howto.html#migrate-from-legacy-upfdata-from-aiida-core.',
+        version=3
+    )
+
 
 REGEX_UPF_VERSION = re.compile(r"""
     \s*<UPF\s+version\s*="
@@ -57,6 +60,8 @@ def get_pseudos_from_structure(structure, family_name):
     """
     from aiida.common.exceptions import MultipleObjectsError, NotExistent
 
+    emit_deprecation()
+
     pseudo_list = {}
     family_pseudos = {}
     family = UpfData.get_upf_group(family_name)
@@ -96,6 +101,8 @@ def upload_upf_family(folder, group_label, group_description, stop_if_existing=T
     from aiida.common.exceptions import UniquenessError
     from aiida.common.files import md5_file
 
+    emit_deprecation()
+
     if not os.path.isdir(folder):
         raise ValueError('folder must be a directory')
 
@@ -204,6 +211,8 @@ def parse_upf(fname, check_filename=True, encoding='utf-8'):
     from aiida.common.exceptions import ParsingError
     from aiida.orm.nodes.data.structure import _valid_symbols
 
+    emit_deprecation()
+
     parsed_data = {}
 
     try:
@@ -278,6 +287,8 @@ def get_or_create(cls, filepath, use_first=False, store_upf=True, backend=None):
 
         from aiida.common.files import md5_file
 
+        emit_deprecation()
+
         if not os.path.isabs(filepath):
             raise ValueError('filepath must be an absolute path')
 
@@ -301,6 +312,10 @@ def get_or_create(cls, filepath, use_first=False, store_upf=True, backend=None):
 
         return (pseudos[0], False)
 
+    def __init__(self, *args, **kwargs):
+        emit_deprecation()
+        super().__init__(*args, **kwargs)
+
     def store(self, *args, **kwargs):  # pylint: disable=signature-differs
         """Store the node, reparsing the file so that the md5 and the element are correctly reset."""
         from aiida.common.exceptions import ParsingError