refactor(release): update make-release script to generate author names

README.md

@@ -216,7 +216,7 @@ How to Cite
 
 ##### ***Software/Code citation for FloPy:***
 
-[Bakker, M., Post, V., Langevin, C.D., Hughes, J.D., White, J.T., Starn, J.J., and Fienen, M.N., 2019, FloPy v3.3.0 — release candidate: U.S. Geological Survey Software Release, 18 November 2019, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
+[Bakker, M., Post, V., Langevin, C. D., Hughes, J. D., White, J. T., Leaf, A. T., Paulinski, S. R., Larsen, J. D., Toews, M. W., Morway, E. D., Bellino, J. C., Starn, J. J., and Fienen, M. N., 2019, FloPy v3.3.0 — release candidate: U.S. Geological Survey Software Release, 12 December 2019, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
 
 
 MODFLOW Resources

binder/environment.yml

@@ -20,5 +20,4 @@ dependencies:
   - rasterio>=1.0
   - rasterstats
   - pyshp
-  - hydrofunctions
   - pip

code.json

@@ -31,7 +31,7 @@
         "laborHours": -1,
         "version": "3.3.0",
         "date": {
-            "metadataLastUpdated": "2019-11-18"
+            "metadataLastUpdated": "2019-12-12"
         },
         "organization": "U.S. Geological Survey",
         "permissions": {

docs/PyPi_release.md

@@ -27,7 +27,7 @@ How to Cite
 
 *Software/Code citation for FloPy:*
 
-[Bakker, M., Post, V., Langevin, C.D., Hughes, J.D., White, J.T., Starn, J.J., and Fienen, M.N., 2019, FloPy v3.3.0 — release candidate: U.S. Geological Survey Software Release, 18 November 2019, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
+[Bakker, M., Post, V., Langevin, C. D., Hughes, J. D., White, J. T., Leaf, A. T., Paulinski, S. R., Larsen, J. D., Toews, M. W., Morway, E. D., Bellino, J. C., Starn, J. J., and Fienen, M. N., 2019, FloPy v3.3.0 — release candidate: U.S. Geological Survey Software Release, 12 December 2019, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
 
 
 Disclaimer

docs/USGS_release.md

@@ -12,7 +12,7 @@ author:
     - Michael W. Toews
     - Eric D. Morway
     - Jason C. Bellino
-    - Jeffrey Starn
+    - Jeffrey J. Starn
     - Michael N. Fienen
 header-includes:
     - \usepackage{fancyhdr}
@@ -23,7 +23,7 @@ header-includes:
     - \fancyhead[CE, CO]{FloPy Release Notes}
     - \fancyfoot[LE, RO]{FloPy version 3.3.0}
     - \fancyfoot[CO, CE]{\thepage\ of \pageref{LastPage}}
-    - \fancyfoot[RE, LO]{11/18/2019}
+    - \fancyfoot[RE, LO]{12/12/2019}
 geometry: margin=0.75in
 ---
 
@@ -56,7 +56,7 @@ How to Cite
 
 ##### ***Software/Code citation for FloPy:***
 
-[Bakker, M., Post, V., Langevin, C.D., Hughes, J.D., White, J.T., Starn, J.J., and Fienen, M.N., 2019, FloPy v3.3.0 — release candidate: U.S. Geological Survey Software Release, 18 November 2019, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
+[Bakker, M., Post, V., Langevin, C. D., Hughes, J. D., White, J. T., Leaf, A. T., Paulinski, S. R., Larsen, J. D., Toews, M. W., Morway, E. D., Bellino, J. C., Starn, J. J., and Fienen, M. N., 2019, FloPy v3.3.0 — release candidate: U.S. Geological Survey Software Release, 12 December 2019, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
 
 
 Disclaimer

docs/make_release.md

@@ -4,18 +4,25 @@ Instructions for making a FloPy release
 ## Make a release branch from develop
 
 1.  Make a release branch from develop (*e.g.* `release3.2.10`)
-2.  Update MODFLOW 6 dfn files in the repository and MODFLOW 6 package classes by running: 
+2.  Update MODFLOW 6 dfn files in the repository and MODFLOW 6 package classes by running:
 
     ```
     python -c 'import flopy; flopy.mf6.utils.generate_classes(branch="master", backup=False)'
     ```
 
+    Evaluate if there are any changes that seem to reduce MODFLOW 6 functionality before committing changes on the release branch.
+
 
 ## Update the release version number
 
 1.  Increment `major`, `minor`, and/or `micro` numbers in `flopy/version.py`, as appropriate.
 
 
+## Update the Software/Code citation for FloPy
+
+1. Update the `authors` list in `release/make-release.py` for the Software/Code citation for FloPy, if required.
+
+
 ## Build USGS release notes
 
 1.  Manually run `make-release.py` in the `release/` directory to update version information using:
@@ -58,43 +65,12 @@ Instructions for making a FloPy release
 3.  Make release on [GitHub website](https://github.com/modflowpy/flopy/releases). Add version changes for [current release](https://github.com/modflowpy/flopy/blob/develop/docs/version_changes.md) from to release text. Publish release.
 
 
-## Update PyPi
-
-1.  Make sure `pypandoc` and `twine` are installed using:
-
-    ```
-    conda search pypandoc
-    conda search twine
-    ```
-
-
-2.  If they are not installed, install one or both using using:
-
-
-    ```
-    conda install pypandoc
-    conda install twine
-    ```
-
-3.  Create the source zip file in a terminal using:
-
-    ```
-    python setup.py sdist --format=zip
-    ```
-
-4.  Upload the release to PyPi using (*make sure* `twine` *is installed using conda*):
-
-    ```
-    twine upload dist/flopy-version.zip
-    ```
-
-
 ## Update flopy-feedstock for conda install
 
 1.  Download the `*.tar.gz` file for the current release from the [GitHub website](https://github.com/modflowpy/flopy/releases).
 
 2.  Calculate the sha256 checksum for the `*.tar.gz` using:
-  
+
     ```
     openssl sha256 flopy-version.tar.gz
     ```
@@ -107,8 +83,8 @@ Instructions for making a FloPy release
     cd /Users/jdhughes/Documents/Development/flopy-feedstock_git
     git fetch upstream
     git checkout master
-    git reset --hard upstream/master  
-    git push origin master --force     
+    git reset --hard upstream/master
+    git push origin master --force
     ```
 
 4.  Rerender the repo using `conda-smithy` (make sure `conda-smithy` is installed using conda):
@@ -124,6 +100,36 @@ Instructions for making a FloPy release
 6.  Make pull request to [flopy-feedstock](https://github.com/conda-forge/flopy-feedstock)
 
 
+## Update PyPi
+
+1.  Make sure `pypandoc` and `twine` are installed using:
+
+    ```
+    conda search pypandoc
+    conda search twine
+    ```
+
+
+2.  If they are not installed, install one or both using using:
+
+
+    ```
+    conda install pypandoc
+    conda install twine
+    ```
+
+3.  Create the source zip file in a terminal using:
+
+    ```
+    python setup.py sdist --format=zip
+    ```
+
+4.  Upload the release to PyPi using (*make sure* `twine` *is installed using conda*):
+
+    ```
+    twine upload dist/flopy-version.zip
+    ```
+
 ## Sync develop and master branches
 
 1.  Merge the `master` branch into the `develop` branch.
@@ -134,8 +140,7 @@ Instructions for making a FloPy release
 
     ```
     python make-release.py
-    ```    
+    ```
 4.  Commit and push the modified `develop` branch.
-
-
-
+
+

flopy/version.py

@@ -1,5 +1,5 @@
 # flopy version file automatically created using...make-release.py
-# created on...November 18, 2019 08:34:13
+# created on...December 12, 2019 16:22:42
 
 major = 3
 minor = 3

release/make-release.py

@@ -13,10 +13,10 @@
 # as the path if the file is in the root repository directory
 paths = ['../flopy', '../',
          '../docs', '../docs',
-         '../', '../']
+         '../', '../', '../docs']
 files = ['version.py', 'README.md',
          'USGS_release.md', 'PyPi_release.md',
-         'code.json', 'DISCLAIMER.md']
+         'code.json', 'DISCLAIMER.md', 'notebook_examples.md']
 
 # check that there are the same number of entries in files and paths
 if len(paths) != len(files):
@@ -27,6 +27,16 @@
 
 pak = 'flopy'
 
+# authors list for Software/Code citation for FloPy
+# author should be defined LastName FirstName MiddleInitial
+# MiddleInitial can be absent. Use spaces instead of commas to separate
+# LastName, FirstName, and MiddleInitial.
+authors = ['Bakker Mark', 'Post Vincent', 'Langevin Christian D',
+           'Hughes Joseph D', 'White Jeremy T', 'Leaf Andrew T',
+           'Paulinski Scott R', 'Larsen Joshua D', 'Toews Michael W',
+           'Morway Eric D', 'Bellino Jason C', 'Starn Jeffrey J',
+           'Fienen Michael N']
+
 approved = '''Disclaimer
 ----------
 
@@ -115,6 +125,32 @@ def get_tag(v0, v1, v2):
     return tag
 
 
+def get_software_citation(version, is_approved):
+    now = datetime.datetime.now()
+    sb = ''
+    if not is_approved:
+        sb = ' — release candidate'
+    line = '['
+    for ipos, author in enumerate(authors):
+        if ipos > 0:
+            line += ', '
+        if ipos == len(authors) - 1:
+            line += 'and '
+        sv = author.split()
+        tauthor = '{}, {}.'.format(sv[0], sv[1][0])
+        if len(sv) > 2:
+            tauthor += ' {}.'.format(sv[2][0])
+        line += tauthor
+    line += ', {}, '.format(now.year) + \
+            'FloPy v{}{}: '.format(version, sb) + \
+            'U.S. Geological Survey Software Release, ' + \
+            '{}, '.format(now.strftime('%d %B %Y')) + \
+            'http://dx.doi.org/10.5066/F7BK19FH]' + \
+            '(http://dx.doi.org/10.5066/F7BK19FH)'
+
+    return line
+
+
 def update_version():
     try:
         fpth = os.path.join(paths[0], files[0])
@@ -157,6 +193,9 @@ def update_version():
     # update README.md with new version information
     update_readme_markdown(vmajor, vminor, vmicro)
 
+    # update notebook_examples.md
+    update_notebook_examples_markdown()
+
     # update code.json
     update_codejson(vmajor, vminor, vmicro)
 
@@ -232,27 +271,20 @@ def update_readme_markdown(vmajor, vminor, vmicro):
                    'modflowpy/flopy/badge.svg?branch={})]'.format(branch) + \
                    '(https://coveralls.io/github/modflowpy/' + \
                    'flopy?branch={})'.format(branch)
+        elif '[Binder]' in line:
+            # [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/modflowpy/flopy.git/develop)
+            line = '[![Binder](https://mybinder.org/badge_logo.svg)]' + \
+                   '(https://mybinder.org/v2/gh/modflowpy/flopy.git/' + \
+                   '{}'.format(branch) + ')'
         elif 'http://dx.doi.org/10.5066/F7BK19FH' in line:
-            now = datetime.datetime.now()
-            sb = ''
-            if not is_approved:
-                sb = ' — release candidate'
-            line = '[Bakker, M., Post, V., Langevin, C.D., Hughes, J.D., ' + \
-                   'White, J.T., Leaf, A.T., Paulinski, S.R., Larsen, J.D., ' + \
-                   'Toews, M.W., Morway, E.D., Bellino, J.C., Starn, J.J., ' + \
-                   'and Fienen, M.N., ' + \
-                   '{}, '.format(now.year) + \
-                   'FloPy v{}{}: '.format(version, sb) + \
-                   'U.S. Geological Survey Software Release, ' + \
-                   '{}, '.format(now.strftime('%d %B %Y')) + \
-                   'http://dx.doi.org/10.5066/F7BK19FH]' + \
-                   '(http://dx.doi.org/10.5066/F7BK19FH)'
+            line = get_software_citation(version, is_approved)
         elif 'Disclaimer' in line:
             line = disclaimer
             terminate = True
         f.write('{}\n'.format(line))
         if terminate:
             break
+
     f.close()
 
     # write disclaimer markdown file
@@ -264,6 +296,34 @@ def update_readme_markdown(vmajor, vminor, vmicro):
     return
 
 
+def update_notebook_examples_markdown():
+    # create disclaimer text
+    is_approved, disclaimer = get_disclaimer()
+
+    # define branch
+    if is_approved:
+        branch = 'master'
+    else:
+        branch = 'develop'
+
+    # read notebook_examples.md into memory
+    fpth = os.path.join(paths[6], files[6])
+    with open(fpth, 'r') as file:
+        lines = [line.rstrip() for line in file]
+
+    # rewrite notebook_examples.md
+    terminate = False
+    f = open(fpth, 'w')
+    for line in lines:
+        if '[Binder]' in line:
+            # [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/modflowpy/flopy.git/develop)
+            line = '[![Binder](https://mybinder.org/badge_logo.svg)]' + \
+                   '(https://mybinder.org/v2/gh/modflowpy/flopy.git/' + \
+                   '{}'.format(branch) + ')'
+        f.write('{}\n'.format(line))
+    f.close()
+
+
 def update_USGSmarkdown(vmajor, vminor, vmicro):
     # get branch
     branch = get_branch()
@@ -295,19 +355,13 @@ def update_USGSmarkdown(vmajor, vminor, vmicro):
     f.write('---\n')
     f.write('title: FloPy Release Notes\n')
     f.write('author:\n')
-    f.write('    - Mark Bakker\n')
-    f.write('    - Vincent Post\n')
-    f.write('    - Christian D. Langevin\n')
-    f.write('    - Joseph D. Hughes\n')
-    f.write('    - Jeremy T. White\n')
-    f.write('    - Andrew T. Leaf\n')
-    f.write('    - Scott R. Paulinski\n')
-    f.write('    - Joshua D. Larsen\n')
-    f.write('    - Michael W. Toews\n')
-    f.write('    - Eric D. Morway\n')
-    f.write('    - Jason C. Bellino\n')
-    f.write('    - Jeffrey Starn\n')
-    f.write('    - Michael N. Fienen\n')
+    for author in authors:
+        sv = author.split()
+        tauthor = '{}'.format(sv[1])
+        if len(sv) > 2:
+            tauthor += ' {}.'.format(sv[2][0])
+        tauthor += ' {}'.format(sv[0])
+        f.write('    - {}\n'.format(tauthor))
     f.write('header-includes:\n')
     f.write('    - \\usepackage{fancyhdr}\n')
     f.write('    - \\usepackage{lastpage}\n')
@@ -330,6 +384,9 @@ def update_USGSmarkdown(vmajor, vminor, vmicro):
             writeline = False
         elif line == 'How to Cite':
             writeline = True
+        elif 'http://dx.doi.org/10.5066/F7BK19FH' in line:
+            writeline = True
+            line = get_software_citation(version, is_approved)
         elif line == 'MODFLOW Resources':
             writeline = False
         elif line == 'Disclaimer':