Merge pull request #87 from thehyve/develop

Release version 0.5.8.

.gitignore

@@ -9,6 +9,7 @@
 dist
 build
 eggs
+.eggs
 parts
 bin
 var
@@ -49,4 +50,6 @@ to_pip.sh
 ~$*.xlsx
 .ipynb_checkpoints/
 !tmtk/arborist/static/jstree/dist
-!examples/*.ipynb
+!examples/*.ipynb
+env/
+venv/

.travis.yml

@@ -8,6 +8,12 @@ matrix:
     env: TOX_ENV=pandas0.22
   - python: 3.7
     env: TOX_ENV=pandas0.23
+  - python: 3.8
+    env: TOX_ENV=pandas0.22
+  - python: 3.8
+    env: TOX_ENV=pandas0.23
+  - python: 3.8
+    env: TOX_ENV=pandas0.24
 
 os:
   - linux
@@ -16,6 +22,7 @@ python:
   - 3.5
   - 3.6
   - 3.7
+  - 3.8
 
 env:
   - TOX_ENV=pandas0.22
@@ -30,4 +37,4 @@ script:
   - tox -e $TOX_ENV
 
 after_success:
-  - codecov
+  - codecov

README.rst

@@ -38,20 +38,20 @@ For general documentation visit `readthedocs`_.
 Installation
 ------------
 
-Installing via Anaconda Cloud or Pypi package managers
+Installing via Anaconda Cloud or Pip package managers
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Anaconda:
 
 .. code:: sh
 
-    $   conda install -c conda-forge tmtk
+    conda install -c conda-forge tmtk
 
-Pypi:
+Pip:
 
 .. code:: sh
 
-    $   pip3 install tmtk
+    pip install tmtk
 
 Installing manually
 ^^^^^^^^^^^^^^^^^^^
@@ -61,20 +61,8 @@ Initialize a virtualenv
 
 .. code:: bash
 
-    $ pip install virtualenv
-    $ virtualenv -p /path/to/python3.x/installation env
-    $ source env/bin/activate
-
-
-For mac users it will most likely be
-
-.. code:: bash
-
-    $ pip install virtualenv
-    $ virtualenv -p python3 env
-    $ source env/bin/activate
-
-or do this using `virtualenvwrapper`_.
+    python3 -m venv env
+    source env/bin/activate
 
 
 Installation from source
@@ -85,38 +73,25 @@ and enable the Arborist Jupyter notebook extension, run:
 
 .. code:: sh
 
-    $   pip3 install -r requirements.txt
-    $   python3 setup.py install
+    pip install -r requirements.txt
+    python setup.py install
 
 or if you want to run the tool from code in development mode:
 
 .. code:: sh
 
-    $   pip3 install -r requirements.txt
-    $   python3 setup.py develop
-    $   jupyter-nbextension install --py tmtk.arborist
-    $   jupyter-serverextension enable tmtk.arborist
+    pip install -r requirements.txt
+    python setup.py develop
+    jupyter-nbextension install --py tmtk.arborist
+    jupyter-serverextension enable tmtk.arborist
 
 
 Requirements
 ^^^^^^^^^^^^
 
-These dependencies will have to be installed:
- - pandas>=0.22.0
- - ipython>=5.3.0
- - jupyter>=1.0.0
- - jupyter-client>=5.0.0
- - jupyter-core>=4.3.0
- - jupyter-console>=5.1.0
- - notebook>=4.4.1
- - requests>=2.13.0
- - tqdm>=4.11.0
- - xlrd>=1.0.0
- - click>=6.0
- - arrow>=0.10.0
-
-Optional dependencies:
- - mygene>=3.0.0
+The dependencies are in ``requirements.txt``,
+optional dependencies are in ``requirements-dev.txt``.
+
 
 Licence
 -------

docs/changelog.rst

@@ -2,6 +2,9 @@
 Changelog
 =========
 
+.. topic::  Version 0.5.8
+
+    * Update dependencies, restrict to pandas < 0.26.
 
 .. topic::  Version 0.5.7
 

requirements-dev.txt

@@ -1 +1 @@
-mygene>=3.0.0
+mygene>=3.1.0,<3.2.0

requirements.txt

@@ -1,12 +1,12 @@
-pandas>=0.22.0
-ipython>=5.3.0
-jupyter>=1.0.0
-jupyter-client>=5.0.0
-jupyter-core>=4.3.0
-jupyter-console>=5.1.0
-notebook>=4.4.1
-requests>=2.13.0
-tqdm>=4.11.0
-xlrd>=1.0.0
-click>=6.0
-arrow>=0.10.0
+pandas>=0.22.0,<0.26.0
+ipython>=7.9.0
+jupyter>=1.0.0,<1.1.0
+jupyter-client>=5.3.4
+jupyter-core>=4.6.1,<4.7.0
+jupyter-console>=5.2.0
+notebook>=5.7.8,<6.1.0
+requests>=2.22.0,<2.23.0
+tqdm>=4.40.0
+xlrd>=1.2.0
+click>=7.0
+arrow>=0.15.4

setup.py

@@ -39,9 +39,9 @@ def run(self):
             return
 
         notebook_version = getattr(notebook, '__version__')
-        if notebook_version is None or notebook_version < '4.2.0':
-            log.info("Version of notebook package should be at least 4.2.0 for Arborist, consider:")
-            log.info("    $ pip3 install --upgrade notebook")
+        if notebook_version is None or notebook_version < '5.7.8':
+            log.info("Version of notebook package should be at least 5.7.8 for Arborist, consider:")
+            log.info("    $ pip install --upgrade notebook")
             log.info('Aborting automated install.')
             return
 
@@ -88,6 +88,11 @@ def run(self):
 
     install_requires=required_packages,
 
+    setup_requires=[
+        # dependency for `python setup.py bdist_wheel`
+        'wheel'
+    ],
+
     entry_points={
         'console_scripts': [
             'transmart-batch = tmtk.utils.batch.__main__:run_batch'
@@ -100,6 +105,7 @@ def run(self):
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
     ],
 
     cmdclass={

tmtk/version.py

@@ -4,5 +4,5 @@
   (see accompanying file LICENSE).
 """
 
-version_info = (0, 5, 7)
+version_info = (0, 5, 8)
 __version__ = '.'.join(map(str, version_info))