upload_datafile: handling of the content (mime) type

.pre-commit-config.yaml

@@ -15,8 +15,12 @@ repos:
     -   id: check-yaml
     -   id: detect-private-key
     -   id: end-of-file-fixer
+    -   id: fix-encoding-pragma
+        args: [--remove]
     -   id: pretty-format-json
         args: [--autofix,--no-sort-keys]
+    -   id: requirements-txt-fixer
+    -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
     rev: 19.10b0
     hooks:
@@ -27,3 +31,8 @@ repos:
     hooks:
     -   id: blacken-docs
         additional_dependencies: [black==19.10b0]
+-   repo: https://github.com/asottile/reorder_python_imports
+    rev: v2.4.0
+    hooks:
+    -   id: reorder-python-imports
+        args: ['--application-directories=.:src', --py36-plus]

.readthedocs.yml

@@ -10,7 +10,9 @@ sphinx:
   configuration:    src/pyDataverse/docs/source/conf.py
 
 # Optionally build your docs in additional formats such as PDF and ePub
-formats:            all
+formats:
+  - epub
+  - pdf
 
 # Optionally set the version of Python and requirements required to build your docs
 python:

.travis.yml

@@ -12,10 +12,6 @@ matrix:
       env:       TOXENV=py38
     - python:    3.6
       env:       TOXENV=docs
-    - python:    3.6
-      env:       TOXENV=coverage
-    - python:    3.6
-      env:       TOXENV=coveralls
 
 branches:
   only:
@@ -26,9 +22,9 @@ before_install:
   - echo $TRAVIS_PYTHON_VERSION
 
 install:
+  - pip install --upgrade pip
   - pip install tox-travis
-  - pip install coverage
-  - pip install coveralls
+  - pip install codecov
   - virtualenv --version
   - easy_install --version
   - pip --version
@@ -38,7 +34,7 @@ script:
   - tox
 
 after_success:
-  - coveralls
+  - codecov
 
 notifications:
   email:

CONTRIBUTING.rst

@@ -229,7 +229,7 @@ you created the branch, check the section on
 :ref:`updating a PR <contributing_changes_update-pull-request>`.
 
 
-From here, you now can move forward to 
+From here, you now can move forward to
 
 - contribute to the documentation (see below)
 - contribute to the :ref:`code base <contributing_code>`
@@ -267,7 +267,7 @@ Some other important things to know about the docs:
 - The pyDataverse documentation consists of two parts:
 
   - the docstrings in the code itself and
-  - the docs in the folder ``src/pyDataverse/doc/``
+  - the docs in the folder ``src/pyDataverse/docs/``
 
 - The docstrings provide a clear explanation of the usage of the individual functions, while the documentation consists of tutorial-like overviews per topic together with some other information (what’s new, installation, this page you're viewing right now, etc).
 - The docstrings follow the `Numpy Docstring Standard <https://numpydoc.readthedocs.io/en/latest/format.html>`_.
@@ -871,6 +871,3 @@ You can find the full release history at :ref:`community_history` and on
 **Versioning**
 
 For pyDataverse, `Semantic versioning <https://semver.org/>`_ is used for releases.
-
-
-.. _contributing_resources:

README.md

@@ -5,4 +5,4 @@
 pyDataverse is a Python module for [Dataverse](http://dataverse.org).
 It helps to access the Dataverse [API's](http://guides.dataverse.org/en/latest/api/index.html) and manipulate, validate, import and export all Dataverse data-types (Dataverse, Dataset, Datafile).
 
-**Find out more: [Read the Docs](https://pydataverse.readthedocs.io/en/latest/)**
+**Find out more: [pyDataverse Documentation](https://pydataverse.readthedocs.io/en/latest/)**

requirements/common.txt

@@ -1,2 +1,2 @@
-requests>=2.12.0
 jsonschema>=3.2.0
+requests>=2.12.0

requirements/development.txt

@@ -1,8 +1,7 @@
-# Requirements for development.
 -r common.txt
--r lint.txt
 -r docs.txt
+-r lint.txt
+-r packaging.txt
 -r tests.txt
-wheel
 pre-commit
-twine
+wheel

requirements/docs.txt

@@ -1,9 +1,7 @@
-# Requirements for documentation test (tox)
--r common.txt
-sphinx==1.7.*
-git+https://github.com/python/python-docs-theme.git#egg=python-docs-theme
 git+https://github.com/pypa/pypa-docs-theme.git#egg=pypa-docs-theme
+git+https://github.com/python/python-docs-theme.git#egg=python-docs-theme
 pydocstyle
-restructuredtext_lint
 pygments
+restructuredtext_lint
 rstcheck
+sphinx==1.7.*

requirements/lint.txt

@@ -1,18 +1,17 @@
-# Requirements for linting tests (tox)
+autopep8
 black==19.10b0
 flake8==3.7.4
-flake8-docstrings==1.5.0
-flake8-rst-docstrings==v0.0.13
-flake8-blind-except==v0.1.1
-flake8-builtins==1.5.3
 flake8-bandit==v2.1.0
+flake8-blind-except==v0.1.1
 flake8-breakpoint==v1.1.0
 flake8-bugbear==20.1.4
+flake8-builtins==1.5.3
 flake8-comprehensions==3.2.3
-flake8-requirements==v1.3.2
-flake8-return==0.3.0
+flake8-docstrings==1.5.0
 flake8-pytest-style==v1.2.1
+flake8-requirements==v1.3.2
+flake8-rst-docstrings==v0.0.13
+mypy==0.790
+Pygments
 pylint
 radon
-mypy==0.790
-autopep8

requirements/packaging.txt

@@ -1,2 +1 @@
-# Requirements for packaging test (tox)
 twine

requirements/tests.txt

@@ -1,6 +1,5 @@
-# Requirements for tests (pytest)
--r common.txt
+codecov
 pytest
 pytest-cov
-tox
 selenium==3.141.0
+tox

setup.cfg

@@ -3,32 +3,36 @@ license_file = LICENSE.txt
 
 [tool:pytest]
 testpaths = tests
-
-[coverage:run]
-source = wheel
-omit = .tox/*
-
-[coverage:report]
-show_missing = true
-
-[radon]
-cc_min = B
+addopts = -v
 
 [flake8]
 max-line-length = 88
 ignore = E129,E203,E501,W503,S101
 exclude =
-    .tox
-    .egg
+    src/pyDataverse/docs
+    src/pyDataverse/schemas
+    src/pyDataverse/templates
     conf.py
     conftest.py
+    __pycache__
+    .mypy_cache
+    .tox
+    .egg
 
 [pylint]
 max-line-length = 88
 
-[pylama:pycodestyle]
-max_line_length = 88
+[coverage:run]
+source=pyDataverse
+
+[coverage:report]
+show_missing = true
+
+[coverage:html]
+directory = docs/coverage/html
+
+[coverage:xml]
+output = coverage.xml
 
-[pylama:pylint]
-max_line_length = 88
-disable = R
+[radon]
+cc_min = B

setup.py

@@ -2,10 +2,11 @@
 import codecs
 import os
 import re
-from setuptools.command.test import test as TestCommand
+import sys
+
 from setuptools import find_packages
 from setuptools import setup
-import sys
+from setuptools.command.test import test as TestCommand
 
 ROOT_DIR = os.path.abspath(os.path.dirname(__file__))
 os.chdir(os.path.normpath(os.path.join(os.path.abspath(__file__), os.pardir)))

src/pyDataverse/__init__.py

@@ -4,8 +4,6 @@
 
 Licensed under the MIT License.
 """
-from __future__ import absolute_import
-
 from requests.packages import urllib3
 
 urllib3.disable_warnings()  # noqa

src/pyDataverse/api.py

@@ -2,16 +2,19 @@
 import json
 import subprocess as sp
 
-from requests import ConnectionError, Response, delete, get, post, put
+from requests import ConnectionError
+from requests import delete
+from requests import get
+from requests import post
+from requests import put
+from requests import Response
 
-from pyDataverse.exceptions import (
-    ApiAuthorizationError,
-    ApiUrlError,
-    DatasetNotFoundError,
-    DataverseNotEmptyError,
-    DataverseNotFoundError,
-    OperationFailedError,
-)
+from pyDataverse.exceptions import ApiAuthorizationError
+from pyDataverse.exceptions import ApiUrlError
+from pyDataverse.exceptions import DatasetNotFoundError
+from pyDataverse.exceptions import DataverseNotEmptyError
+from pyDataverse.exceptions import DataverseNotFoundError
+from pyDataverse.exceptions import OperationFailedError
 
 
 class Api:
@@ -1639,7 +1642,7 @@ def get_datafile_metadata(
             # CHECK: Its not really clear, if the version query can also be done via ID.
         return self.get_request(url, auth=auth)
 
-    def upload_datafile(self, identifier, filename, json_str=None, is_pid=True):
+    def upload_datafile(self, identifier, filename, json_str=None, is_pid=True, content_type='application/octet-stream'):
         """Add file to a dataset.
 
         Add a file to an existing Dataset. Description and tags are optional:
@@ -1666,6 +1669,8 @@ def upload_datafile(self, identifier, filename, json_str=None, is_pid=True):
             Metadata as JSON string.
         is_pid : bool
             ``True`` to use persistent identifier. ``False``, if not.
+        content_type : str
+            MIME type. Defaults to ``application/octet-stream``; this will prompt Dataverse to attempt to identify the MIME type of the file more accurately. 
 
         Returns
         -------
@@ -1680,7 +1685,7 @@ def upload_datafile(self, identifier, filename, json_str=None, is_pid=True):
         else:
             url += "/datasets/{0}/add".format(identifier)
 
-        files = {"file": open(filename, "rb")}
+        files = {"file": (filename, open(filename, "rb"), content_type)}
         return self.post_request(
             url, data={"jsonData": json_str}, files=files, auth=True
         )
@@ -2083,6 +2088,7 @@ def get_children(
         - Unify tree and models
 
         """
+        # print(self.base_url_api)
         children = []
 
         if children_types is None:
@@ -2181,7 +2187,7 @@ def get_user(self):
 
         https://guides.dataverse.org/en/latest/api/native-api.html#get-user-information-in-json-format
         """
-        url = f"{self.base_url}/users/:me"
+        url = f"{self.base_url_api_native}/users/:me"
         return self.get_request(url, auth=True)
 
     def redetect_file_type(

src/pyDataverse/docs/source/conf.py

@@ -3,21 +3,18 @@
 # This file does only contain a selection of the most common options. For a
 # full list see the documentation:
 # http://www.sphinx-doc.org/en/master/config
-
 # -- 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.
 #
 # sys.path.insert(0, os.path.abspath('../../'))
-
 # -- Project information -----------------------------------------------------
-
-import pyDataverse
-from datetime import date
 import os
 import sys
+from datetime import date
+
+import pyDataverse
 
 sys.path.insert(0, os.path.abspath("../../.."))
 

src/pyDataverse/docs/source/index.rst

@@ -39,7 +39,7 @@ Release v\ |version|.
 
 .. _homepage_description:
 
-**pyDataverse** is a Python module for `Dataverse <http://dataverse.org>`_ you can use for:  
+**pyDataverse** is a Python module for `Dataverse <http://dataverse.org>`_ you can use for:
 
 - accessing the Dataverse `API's <http://guides.dataverse.org/en/latest/api/index.html>`_
 - manipulating and using the Dataverse (meta)data - Dataverses, Datasets, Datafiles

src/pyDataverse/docs/source/reference.rst

@@ -10,6 +10,8 @@ Where pyDataverse depends on external libraries, we document the most
 important right here and provide links to the canonical documentation outside of scope.
 
 
+.. _reference_api:
+
 API Interface
 -----------------------------
 
@@ -19,6 +21,8 @@ Access all of Dataverse APIs.
    :members:
 
 
+.. _reference_models:
+
 Models Interface
 -----------------------------
 
@@ -29,6 +33,8 @@ and `Datafile`). This includes import, export and manipulation.
   :inherited-members:
 
 
+.. _reference_utils:
+
 Utils Interface
 -----------------------------
 
@@ -38,6 +44,8 @@ Helper functions.
   :members:
 
 
+.. _reference_exceptions:
+
 Exceptions
 -----------------------------
 

src/pyDataverse/docs/source/user/advanced-usage.rst

@@ -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`.
 
 ::