Merge pull request #115 from UC-Davis-molecular-computing/dev

Dev

.github/workflows/python-publish.yml

@@ -0,0 +1,32 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  push:
+    branches:
+      - "master"
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

README.md

@@ -37,15 +37,17 @@ Please report issues in the web interface at the [scadnano web interface GitHub
 
 ## Installation
 
-The scadnano Python package requires Python version 3.7 or later. If you do not have that version (or later) of Python installed, follow [this link](https://www.python.org/downloads/) to install it. 
+The scadnano Python package requires Python version 3.7 or later. If you do not have that version (or later) of Python installed, follow [this link](https://www.python.org/downloads/) to install it. To check your current version of Python, open a command line and type
 
-If you are using Python 3.6 and do not wish to upgrade, with some effort you can install a package that give the required features.
-The Python 3.7 module that is not present in 3.6 is the 
-[dataclasses](https://docs.python.org/3/library/dataclasses.html) module.
-You can install a backported library for it: 
-[dataclasses backport](https://pypi.org/project/dataclasses/) (this library appears to require at least Python version 3.6)
+```
+python --version
+```
 
-Furthermore, the [typing](https://docs.python.org/3/library/typing.html) module was present in Python 3.5, but scadnano requires at least version Python 3.6.2.
+If you are using Python 3.6 and do not wish to upgrade, you can install a package providing the required features.
+There is a Python 3.7 module used by scadnano, which is not present in 3.6: the
+[dataclasses](https://docs.python.org/3/library/dataclasses.html) module.
+If you have at least Python version 3.6, you can install a backported library providing this module: 
+[dataclasses backport](https://pypi.org/project/dataclasses/)
 
 Once Python is installed (and the dataclasses backport if you have Python version 3.6), there are two ways you can install the scadnano Python package:
 
@@ -64,6 +66,27 @@ Once Python is installed (and the dataclasses backport if you have Python versio
     or 
     https://www.liquidweb.com/kb/install-pip-windows/.
 
+    First, check your version of `pip` by typing 
+    ```
+    pip --version
+    ```
+    It should say something like 
+    ```
+    pip 19.3.1 from ...lib\site-packages\pip (python 3.8)
+    ```
+    If the version of Python at the end is Python 3.7 or higher, you are good. If it is version 2.7 or lower, type
+    ```
+    pip3 --version
+    ```
+    If that works and shows Python 3.7 or higher, you are good, but you should type `pip3` in the subsequent instructions instead of `pip`.
+    
+    If it shows Python 3.6, install the [dataclasses backport module](https://pypi.org/project/dataclasses/) via
+    ```
+    pip install dataclasses
+    ```
+    If it shows Python 3.5 or lower, then you will need to upgrade your Python version (recommended Python 3.7 or higher).
+
+    
 2. download
 
     *Note:* If you are reading this on the PyPI website, the links below won't work. They are relative links intended to be read on the [GitHub README page](https://github.com/UC-Davis-molecular-computing/scadnano-python-package#readme).
@@ -75,7 +98,7 @@ Once Python is installed (and the dataclasses backport if you have Python versio
     * *optional*: [origami_rectangle.py](scadnano/origami_rectangle.py); This can help create origami rectangles, but it is not necessary to use scadnano.
     * *optional*: [_version.py](scadnano/_version.py) This ensures that the current version number is written into any `.dna` files written by the library; otherwise it may be out of date. (Which should not matter for the most part.)
     
-    The scadnano package uses the Python package [xlwt](https://pypi.org/project/xlwt/) to write Excel files, so in order to call the method [`DNADesign.write_idt_plate_excel_file()`](https://scadnano-python-package.readthedocs.io/#scadnano.DNADesign.write_idt_plate_excel_file) to export an Excel file with DNA sequences, xlwt must be installed. To install, type `pip install xlwt` at the command line.
+    The scadnano package uses the Python package [xlwt](https://pypi.org/project/xlwt/) to write Excel files, so xlwt must be installed in order to call the method [`DNADesign.write_idt_plate_excel_file()`](https://scadnano-python-package.readthedocs.io/#scadnano.DNADesign.write_idt_plate_excel_file) to export an Excel file with DNA sequences. To install xlwt, type `pip install xlwt` at the command line. (If you instead use pip to install the scadnano package, xlwt will be automatically installed.)
 
 
 

scadnano/_version.py

@@ -3,4 +3,4 @@
 
 # The following line *must* be the last in the module, exactly as formatted:
 # XXX: REMEMBER TO CHANGE VERSION IN scadnano.py also, for users who do not install from PyPI
-__version__ = "0.9.9"
+__version__ = "0.9.10"

scadnano/scadnano.py

@@ -64,7 +64,7 @@
     from ._version import __version__
 except ImportError:
     # this is so scadnano.py file works without _version.py being present, in case user downloads it
-    __version__ = "0.9.9"
+    __version__ = "0.9.10"
 
 StrandLabel = TypeVar('StrandLabel')
 DomainLabel = TypeVar('DomainLabel')