Merge pull request #45 from dvklopfenstein/dvk

Use pip3; Added src and src/bin modules to pmidcite package
dvklopfenstein · Nov 28, 2022 · c13a9c5 · c13a9c5
2 parents f66ff55 + 489c2c3
commit c13a9c5
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Showing 8 changed files with 27 additions and 8 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,7 @@
 ## Summary
 
 * [**Unreleased**](#unreleased)
+* [**Release 2022-11-26 v0.0.38**](#release-2022-11-28-v0039) pip3, not pip from Python2
 * [**Release 2022-11-26 v0.0.38**](#release-2022-11-26-v0038) Added instructions, and console_script to run script, icite
 * [**Release 2022-09-27 v0.0.37**](#release-2022-09-27-v0037) Remove unused package in setup.py
 * [**Release 2022-07-03 v0.0.36**](#release-2022-07-03-v0036) Change citation count on GitHub repo card
@@ -40,6 +41,10 @@
 
 ### Unreleased
 
+### release 2022-11-29 v0.0.39
+* CHANGED `pip install .` to `pip3 install .` in makefile and README.md
+* ADDED `src` and `src.bin` to package modules
+
 ### release 2022-11-26 v0.0.38
 * ADDED instructions for loading locally to README.md [#43](https://github.com/dvklopfenstein/pmidcite/issues/43)
 * ADDED entry_points, console_scripts, icite to setup.py [#42](https://github.com/dvklopfenstein/pmidcite/issues/42)

diff --git a/README.md b/README.md
@@ -348,13 +348,13 @@ $ grep TOP log/icite/Osbourn_Anne.txt | awk '{print $7 " " $8}' | scatter.py
 
 ## Installation
 To install from [**PyPI**](https://pypi.org/project/pmidcite/)    
-```$ pip install pmidcite```
+```$ pip3 install pmidcite```
 
 To install locally
 ```
 $ git clone https://github.com/dvklopfenstein/pmidcite.git
 $ cd ./pmidcite
-$ pip install .
+$ pip3 install .
 ```
 
 

diff --git a/docs/index.md b/docs/index.md
@@ -112,7 +112,14 @@ https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilitie
 
 ## Installation
 To install from [**PyPI**](https://pypi.org/project/pmidcite/)    
-```pip install pmidcite```
+```pip3 install pmidcite```
+
+To install locally
+```
+$ git clone https://github.com/dvklopfenstein/pmidcite.git
+$ cd ./pmidcite
+$ pip3 install .
+```
 
 # Contact
 [email protected]    

diff --git a/makefile b/makefile
@@ -1,7 +1,7 @@
 PYTHON = python3
 
 install:
-	pip install .
+	pip3 install .
 
 py:
 	find src -name \*.py

diff --git a/setup.py b/setup.py
@@ -23,21 +23,26 @@
     'pmidcite.icite',
     'pmidcite.icite.dnldr',
     'pmidcite.plot',
+    'src',
+    'src.bin',
 ]
 
 PACKAGE_DIRS = {p:join('src', *p.split('.')) for p in PACKAGES}
 
 def get_long_description():
     """Return the contents of the README.md as a string"""
     dir_cur = abspath(dirname(__file__))
-    with open(join(dir_cur, 'README.md'), encoding='utf-8') as ifstrm:
-        return ifstrm.read()
+    # python3
+    #with open(join(dir_cur, 'README.md'), encoding='utf-8') as ifstrm:
+    # python3 or python2
+    with open(join(dir_cur, 'README.md'), 'rb') as ifstrm:
+        return ifstrm.read().decode("UTF-8")
 
 
 setup(
     name=NAME,
     ## version=versioneer.get_version(),
-    version='0.0.38',
+    version='0.0.39',
     author='DV Klopfenstein, PhD',
     author_email='[email protected]',
     ## cmdclass=versioneer.get_cmdclass(),

diff --git a/src/__init__.py b/src/__init__.py
@@ -0,0 +1 @@
+"""Source"""
diff --git a/src/bin/__init__.py b/src/bin/__init__.py
@@ -0,0 +1 @@
+"""Scripts module"""
diff --git a/src/pmidcite/__version__.py b/src/pmidcite/__version__.py
@@ -1,3 +1,3 @@
 """Version of pmidcite project"""
 
-__version__ = '0.0.38'
+__version__ = '0.0.39'