move source code from src to root

gdcc · May 7, 2024 · 11ace57 · 11ace57
1 parent 8b011e7
commit 11ace57
Show file tree

Hide file tree

Showing 33 changed files with 71 additions and 64 deletions.
diff --git a/src/pyDataverse/__init__.py → pyDataverse/__init__.py b/src/pyDataverse/__init__.py → pyDataverse/__init__.py
@@ -7,15 +7,12 @@
 
 from __future__ import absolute_import
 
-import urllib3
-
-urllib3.disable_warnings()  # noqa
 
 __author__ = "Stefan Kasberger"
 __email__ = "[email protected]"
 __copyright__ = "Copyright (c) 2019 Stefan Kasberger"
 __license__ = "MIT License"
-__version__ = "0.3.1"
+__version__ = "0.3.2"
 __url__ = "https://github.com/GDCC/pyDataverse"
 __download_url__ = "https://pypi.python.org/pypi/pyDataverse"
 __description__ = "A Python module for Dataverse."
diff --git a/src/pyDataverse/api.py → pyDataverse/api.py b/src/pyDataverse/api.py → pyDataverse/api.py
diff --git a/...ocs/source/_images/collection_dataset.png → ...ocs/source/_images/collection_dataset.png b/...ocs/source/_images/collection_dataset.png → ...ocs/source/_images/collection_dataset.png
diff --git a/src/pyDataverse/docs/source/_static/.gitkeep → pyDataverse/docs/source/_static/.gitkeep b/src/pyDataverse/docs/source/_static/.gitkeep → pyDataverse/docs/source/_static/.gitkeep
diff --git a/...averse/docs/source/_templates/layout.html → ...averse/docs/source/_templates/layout.html b/...averse/docs/source/_templates/layout.html → ...averse/docs/source/_templates/layout.html
diff --git a/...docs/source/_templates/sidebar_intro.html → ...docs/source/_templates/sidebar_intro.html b/...docs/source/_templates/sidebar_intro.html → ...docs/source/_templates/sidebar_intro.html
diff --git a/...rce/_templates/sidebar_related-links.html → ...rce/_templates/sidebar_related-links.html b/...rce/_templates/sidebar_related-links.html → ...rce/_templates/sidebar_related-links.html
diff --git a/...taverse/docs/source/community/contact.rst → ...taverse/docs/source/community/contact.rst b/...taverse/docs/source/community/contact.rst → ...taverse/docs/source/community/contact.rst
diff --git a/...averse/docs/source/community/releases.rst → ...averse/docs/source/community/releases.rst b/...averse/docs/source/community/releases.rst → ...averse/docs/source/community/releases.rst
diff --git a/src/pyDataverse/docs/source/conf.py → pyDataverse/docs/source/conf.py b/src/pyDataverse/docs/source/conf.py → pyDataverse/docs/source/conf.py
diff --git a/...docs/source/contributing/contributing.rst → ...docs/source/contributing/contributing.rst b/...docs/source/contributing/contributing.rst → ...docs/source/contributing/contributing.rst
diff --git a/src/pyDataverse/docs/source/index.rst → pyDataverse/docs/source/index.rst b/src/pyDataverse/docs/source/index.rst → pyDataverse/docs/source/index.rst
diff --git a/src/pyDataverse/docs/source/reference.rst → pyDataverse/docs/source/reference.rst b/src/pyDataverse/docs/source/reference.rst → pyDataverse/docs/source/reference.rst
diff --git a/...erse/docs/source/snippets/pip-install.rst → ...erse/docs/source/snippets/pip-install.rst b/...erse/docs/source/snippets/pip-install.rst → ...erse/docs/source/snippets/pip-install.rst
diff --git a/...rse/docs/source/snippets/requirements.rst → ...rse/docs/source/snippets/requirements.rst b/...rse/docs/source/snippets/requirements.rst → ...rse/docs/source/snippets/requirements.rst
diff --git a/...cs/source/snippets/warning_production.rst → ...cs/source/snippets/warning_production.rst b/...cs/source/snippets/warning_production.rst → ...cs/source/snippets/warning_production.rst
diff --git a/...verse/docs/source/user/advanced-usage.rst → ...verse/docs/source/user/advanced-usage.rst b/...verse/docs/source/user/advanced-usage.rst → ...verse/docs/source/user/advanced-usage.rst
@@ -42,7 +42,7 @@ Prepare
 
 **Additional Resources**
 
-- CSV templates from ``src/pyDataverse/templates/`` are used (see :ref:`CSV templates <user_csv-templates>`)
+- CSV templates from ``pyDataverse/templates/`` are used (see :ref:`CSV templates <user_csv-templates>`)
 - Data from ``tests/data/user-guide/`` is used (`GitHub repo <https://github.com/gdcc/pyDataverse/tree/master/tests/data/user-guide>`_)
 
 
@@ -101,10 +101,10 @@ converts boolean values, and loads JSON cells properly.
 Once we have the data in Python, we can easily import the data into
 pyDataverse.
 
-For this, loop over each Dataset :class:`dict`, to: 
+For this, loop over each Dataset :class:`dict`, to:
 
 #. Instantiate an empty :class:`Dataset <pyDataverse.models.Dataset>`
-#. add the data with :meth:`set() <pyDataverse.models.Dataset.set>` and 
+#. add the data with :meth:`set() <pyDataverse.models.Dataset.set>` and
 #. append the instance to a :class:`list`.
 
 ::

diff --git a/...ataverse/docs/source/user/basic-usage.rst → pyDataverse/docs/source/user/basic-usage.rst b/...ataverse/docs/source/user/basic-usage.rst → pyDataverse/docs/source/user/basic-usage.rst
diff --git a/...averse/docs/source/user/csv-templates.rst → ...averse/docs/source/user/csv-templates.rst b/...averse/docs/source/user/csv-templates.rst → ...averse/docs/source/user/csv-templates.rst
@@ -71,12 +71,12 @@ There is also a more detailed tutorial on how to use the CSV templates
 for mass imports in the
 :ref:`User Guide - Advanced <advanced-usage_data-migration>`.
 
-The CSV templates can be found in ``src/pyDataverse/templates/``
-(`GitHub repo <https://github.com/gdcc/pyDataverse/tree/master/src/pyDataverse/templates>`_):
+The CSV templates can be found in ``pyDataverse/templates/``
+(`GitHub repo <https://github.com/gdcc/pyDataverse/tree/master/pyDataverse/templates>`_):
 
-- `dataverses.csv <https://raw.githubusercontent.com/gdcc/pyDataverse/master/src/pyDataverse/templates/dataverses.csv>`_
-- `datasets.csv <https://raw.githubusercontent.com/gdcc/pyDataverse/master/src/pyDataverse/templates/datasets.csv>`_
-- `datafiles.csv <https://raw.githubusercontent.com/gdcc/pyDataverse/master/src/pyDataverse/templates/datafiles.csv>`_
+- `dataverses.csv <https://raw.githubusercontent.com/gdcc/pyDataverse/master/pyDataverse/templates/dataverses.csv>`_
+- `datasets.csv <https://raw.githubusercontent.com/gdcc/pyDataverse/master/pyDataverse/templates/datasets.csv>`_
+- `datafiles.csv <https://raw.githubusercontent.com/gdcc/pyDataverse/master/pyDataverse/templates/datafiles.csv>`_
 
 
 .. _user_csv-templates_usage_create-csv:

diff --git a/src/pyDataverse/docs/source/user/faq.rst → pyDataverse/docs/source/user/faq.rst b/src/pyDataverse/docs/source/user/faq.rst → pyDataverse/docs/source/user/faq.rst
diff --git a/...taverse/docs/source/user/installation.rst → ...taverse/docs/source/user/installation.rst b/...taverse/docs/source/user/installation.rst → ...taverse/docs/source/user/installation.rst
diff --git a/...yDataverse/docs/source/user/resources.rst → pyDataverse/docs/source/user/resources.rst b/...yDataverse/docs/source/user/resources.rst → pyDataverse/docs/source/user/resources.rst
diff --git a/...yDataverse/docs/source/user/use-cases.rst → pyDataverse/docs/source/user/use-cases.rst b/...yDataverse/docs/source/user/use-cases.rst → pyDataverse/docs/source/user/use-cases.rst
diff --git a/src/pyDataverse/exceptions.py → pyDataverse/exceptions.py b/src/pyDataverse/exceptions.py → pyDataverse/exceptions.py
diff --git a/src/pyDataverse/models.py → pyDataverse/models.py b/src/pyDataverse/models.py → pyDataverse/models.py
@@ -1,4 +1,5 @@
 """Dataverse data-types data model."""
+
 from __future__ import absolute_import
 
 import json
@@ -103,7 +104,9 @@ def validate_json(self, filename_schema=None):
         assert isinstance(filename_schema, str)
 
         return validate_data(
-            json.loads(self.json(validate=False)), filename_schema, file_format="json",
+            json.loads(self.json(validate=False)),
+            filename_schema,
+            file_format="json",
         )
 
     def from_json(
@@ -867,7 +870,6 @@ def from_json(
                         )
 
             if "metadataBlocks" in json_dict["datasetVersion"]:
-
                 # citation
                 if "citation" in json_dict["datasetVersion"]["metadataBlocks"]:
                     citation = json_dict["datasetVersion"]["metadataBlocks"]["citation"]
@@ -954,7 +956,8 @@ def from_json(
 
                     if "displayName" in socialscience:
                         self.__setattr__(
-                            "socialscience_displayName", socialscience["displayName"],
+                            "socialscience_displayName",
+                            socialscience["displayName"],
                         )
 
                     for field in socialscience["fields"]:
@@ -966,27 +969,27 @@ def from_json(
                         elif field["typeName"] == "targetSampleSize":
                             data["targetSampleSize"] = {}
                             if "targetSampleActualSize" in field["value"]:
-                                data["targetSampleSize"][
-                                    "targetSampleActualSize"
-                                ] = field["value"]["targetSampleActualSize"]["value"]
+                                data["targetSampleSize"]["targetSampleActualSize"] = (
+                                    field["value"]["targetSampleActualSize"]["value"]
+                                )
                             if "targetSampleSizeFormula" in field["value"]:
-                                data["targetSampleSize"][
-                                    "targetSampleSizeFormula"
-                                ] = field["value"]["targetSampleSizeFormula"]["value"]
+                                data["targetSampleSize"]["targetSampleSizeFormula"] = (
+                                    field["value"]["targetSampleSizeFormula"]["value"]
+                                )
                         elif field["typeName"] == "socialScienceNotes":
                             data["socialScienceNotes"] = {}
                             if "socialScienceNotesType" in field["value"]:
-                                data["socialScienceNotes"][
-                                    "socialScienceNotesType"
-                                ] = field["value"]["socialScienceNotesType"]["value"]
+                                data["socialScienceNotes"]["socialScienceNotesType"] = (
+                                    field["value"]["socialScienceNotesType"]["value"]
+                                )
                             if "socialScienceNotesSubject" in field["value"]:
                                 data["socialScienceNotes"][
                                     "socialScienceNotesSubject"
                                 ] = field["value"]["socialScienceNotesSubject"]["value"]
                             if "socialScienceNotesText" in field["value"]:
-                                data["socialScienceNotes"][
-                                    "socialScienceNotesText"
-                                ] = field["value"]["socialScienceNotesText"]["value"]
+                                data["socialScienceNotes"]["socialScienceNotesText"] = (
+                                    field["value"]["socialScienceNotesText"]["value"]
+                                )
                         else:
                             print(
                                 "Attribute {0} not valid for import (dv_up).".format(
@@ -1200,7 +1203,10 @@ def json(self, data_format=None, validate=True, filename_schema=None):
                     )
 
             # Generate fields attributes
-            for (key, val,) in self.__attr_import_dv_up_citation_fields_arrays.items():
+            for (
+                key,
+                val,
+            ) in self.__attr_import_dv_up_citation_fields_arrays.items():
                 if key in data_dict:
                     v = data_dict[key]
                     citation["fields"].append(
@@ -1341,25 +1347,25 @@ def json(self, data_format=None, validate=True, filename_schema=None):
                 if "targetSampleActualSize" in target_sample_size:
                     if target_sample_size["targetSampleActualSize"] is not None:
                         tmp_dict["targetSampleActualSize"] = {}
-                        tmp_dict["targetSampleActualSize"][
-                            "typeName"
-                        ] = "targetSampleActualSize"
+                        tmp_dict["targetSampleActualSize"]["typeName"] = (
+                            "targetSampleActualSize"
+                        )
                         tmp_dict["targetSampleActualSize"]["multiple"] = False
                         tmp_dict["targetSampleActualSize"]["typeClass"] = "primitive"
-                        tmp_dict["targetSampleActualSize"][
-                            "value"
-                        ] = target_sample_size["targetSampleActualSize"]
+                        tmp_dict["targetSampleActualSize"]["value"] = (
+                            target_sample_size["targetSampleActualSize"]
+                        )
                 if "targetSampleSizeFormula" in target_sample_size:
                     if target_sample_size["targetSampleSizeFormula"] is not None:
                         tmp_dict["targetSampleSizeFormula"] = {}
-                        tmp_dict["targetSampleSizeFormula"][
-                            "typeName"
-                        ] = "targetSampleSizeFormula"
+                        tmp_dict["targetSampleSizeFormula"]["typeName"] = (
+                            "targetSampleSizeFormula"
+                        )
                         tmp_dict["targetSampleSizeFormula"]["multiple"] = False
                         tmp_dict["targetSampleSizeFormula"]["typeClass"] = "primitive"
-                        tmp_dict["targetSampleSizeFormula"][
-                            "value"
-                        ] = target_sample_size["targetSampleSizeFormula"]
+                        tmp_dict["targetSampleSizeFormula"]["value"] = (
+                            target_sample_size["targetSampleSizeFormula"]
+                        )
                 socialscience["fields"].append(
                     {
                         "typeName": "targetSampleSize",
@@ -1376,36 +1382,36 @@ def json(self, data_format=None, validate=True, filename_schema=None):
                 if "socialScienceNotesType" in social_science_notes:
                     if social_science_notes["socialScienceNotesType"] is not None:
                         tmp_dict["socialScienceNotesType"] = {}
-                        tmp_dict["socialScienceNotesType"][
-                            "typeName"
-                        ] = "socialScienceNotesType"
+                        tmp_dict["socialScienceNotesType"]["typeName"] = (
+                            "socialScienceNotesType"
+                        )
                         tmp_dict["socialScienceNotesType"]["multiple"] = False
                         tmp_dict["socialScienceNotesType"]["typeClass"] = "primitive"
-                        tmp_dict["socialScienceNotesType"][
-                            "value"
-                        ] = social_science_notes["socialScienceNotesType"]
+                        tmp_dict["socialScienceNotesType"]["value"] = (
+                            social_science_notes["socialScienceNotesType"]
+                        )
                 if "socialScienceNotesSubject" in social_science_notes:
                     if social_science_notes["socialScienceNotesSubject"] is not None:
                         tmp_dict["socialScienceNotesSubject"] = {}
-                        tmp_dict["socialScienceNotesSubject"][
-                            "typeName"
-                        ] = "socialScienceNotesSubject"
+                        tmp_dict["socialScienceNotesSubject"]["typeName"] = (
+                            "socialScienceNotesSubject"
+                        )
                         tmp_dict["socialScienceNotesSubject"]["multiple"] = False
                         tmp_dict["socialScienceNotesSubject"]["typeClass"] = "primitive"
-                        tmp_dict["socialScienceNotesSubject"][
-                            "value"
-                        ] = social_science_notes["socialScienceNotesSubject"]
+                        tmp_dict["socialScienceNotesSubject"]["value"] = (
+                            social_science_notes["socialScienceNotesSubject"]
+                        )
                 if "socialScienceNotesText" in social_science_notes:
                     if social_science_notes["socialScienceNotesText"] is not None:
                         tmp_dict["socialScienceNotesText"] = {}
-                        tmp_dict["socialScienceNotesText"][
-                            "typeName"
-                        ] = "socialScienceNotesText"
+                        tmp_dict["socialScienceNotesText"]["typeName"] = (
+                            "socialScienceNotesText"
+                        )
                         tmp_dict["socialScienceNotesText"]["multiple"] = False
                         tmp_dict["socialScienceNotesText"]["typeClass"] = "primitive"
-                        tmp_dict["socialScienceNotesText"][
-                            "value"
-                        ] = social_science_notes["socialScienceNotesText"]
+                        tmp_dict["socialScienceNotesText"]["value"] = (
+                            social_science_notes["socialScienceNotesText"]
+                        )
                 socialscience["fields"].append(
                     {
                         "typeName": "socialScienceNotes",
@@ -1456,7 +1462,10 @@ def json(self, data_format=None, validate=True, filename_schema=None):
                     )
 
             # Generate fields attributes
-            for (key, val,) in self.__attr_import_dv_up_journal_fields_arrays.items():
+            for (
+                key,
+                val,
+            ) in self.__attr_import_dv_up_journal_fields_arrays.items():
                 if key in data_dict:
                     journal["fields"].append(
                         {
@@ -1469,9 +1478,9 @@ def json(self, data_format=None, validate=True, filename_schema=None):
 
             data["datasetVersion"]["metadataBlocks"]["citation"] = citation
             if "socialscience" in locals():
-                data["datasetVersion"]["metadataBlocks"][
-                    "socialscience"
-                ] = socialscience
+                data["datasetVersion"]["metadataBlocks"]["socialscience"] = (
+                    socialscience
+                )
             if "geospatial" in locals():
                 data["datasetVersion"]["metadataBlocks"]["geospatial"] = geospatial
             if "journal" in locals():

diff --git a/.../schemas/json/datafile_upload_schema.json → .../schemas/json/datafile_upload_schema.json b/.../schemas/json/datafile_upload_schema.json → .../schemas/json/datafile_upload_schema.json
diff --git a/...s/json/dataset_upload_default_schema.json → ...s/json/dataset_upload_default_schema.json b/...s/json/dataset_upload_default_schema.json → ...s/json/dataset_upload_default_schema.json
diff --git a/...schemas/json/dataverse_upload_schema.json → ...schemas/json/dataverse_upload_schema.json b/...schemas/json/dataverse_upload_schema.json → ...schemas/json/dataverse_upload_schema.json
diff --git a/...Dataverse/schemas/json/dspace_schema.json → pyDataverse/schemas/json/dspace_schema.json b/...Dataverse/schemas/json/dspace_schema.json → pyDataverse/schemas/json/dspace_schema.json
diff --git a/src/pyDataverse/templates/datafiles.csv → pyDataverse/templates/datafiles.csv b/src/pyDataverse/templates/datafiles.csv → pyDataverse/templates/datafiles.csv
diff --git a/src/pyDataverse/templates/datasets.csv → pyDataverse/templates/datasets.csv b/src/pyDataverse/templates/datasets.csv → pyDataverse/templates/datasets.csv
diff --git a/src/pyDataverse/templates/dataverses.csv → pyDataverse/templates/dataverses.csv b/src/pyDataverse/templates/dataverses.csv → pyDataverse/templates/dataverses.csv
diff --git a/src/pyDataverse/utils.py → pyDataverse/utils.py b/src/pyDataverse/utils.py → pyDataverse/utils.py
@@ -1,4 +1,5 @@
 """Helper functions."""
+
 import csv
 import json
 import os
@@ -585,13 +586,13 @@ def dataverse_tree_walker(
     datasets = []
     datafiles = []
 
-    if type(data) == list:
+    if isinstance(data, list):
         for elem in data:
             dv, ds, df = dataverse_tree_walker(elem)
             dataverses += dv
             datasets += ds
             datafiles += df
-    elif type(data) == dict:
+    elif isinstance(data, dict):
         if data["type"] == "dataverse":
             dv_tmp = {}
             for key in dv_keys: