Release 0.5.18. Includes numerous documentation, script and config file tweaks.

Author: gklyne

README.md

@@ -6,16 +6,16 @@ annalist
 
 A free-form web linked data notebook and prototyping tool - "Data management for little guys"
 
-Current status (2019-05-10):  public prototype, released for evaluation and feedback, feature freeze for version 1 release.  Deployable as web-facing service using Apache2 or nginx for HTTPS handling (proxying).
+Current status (2022-04-09):  prototype software for evaluation and feedback, feature freeze for version 1 release.  Deployable as web-facing service using Apache2 or nginx for HTTPS handling (proxying).
 
 For information about the current release, please refer to the [V0.5 release notes](documents/release-notes/release-v0.5.md)
 
 NOTE: most recent stable software release is on the Git `master` branch; current development work is on the `develop` branch.
 
-Demo system home page
----------------------
+Home page
+---------
 
-For general information about Annalist, and demonstration system links, see the [Annalist demonstration system home page](http://annalist.net/).
+For general information about Annalist, and demonstration system links, see the [Annalist home page](http://annalist.net/).
 
 Quick-start
 -----------
@@ -85,7 +85,7 @@ Acknowledgements
 
 Ideas motivating the creation of Annalist arose from discussions with past colleagues in the Zoology department at Oxford University, particularly Dr David Shotton who led the BioImage project, and Dr Helen White-Cooper who patiently explained her processes and data handling needs as a genomic researcher.
 
-David Flanders, formerly of JISC, provided encouragement and support for the development of software tools to support academic activities, and in particular raising the profile of engineering and management skills needed to create effective software tools for academics.  A previous project, [Shuffl](https://code.google.com/p/shuffl/), conducted under a JISC Rapid Innovation program that he ran, trialled some early ideas that have contributed to the development of Annalist (since migrated to [GitHub](https://github.com/gklyne/shuffl/tree/master) and [GitHub wiki](https://github.com/gklyne/shuffl/blob/wiki/ProjectHome.md)). 
+David Flanders, formerly of JISC, provided encouragement and support for the development of software tools to support academic activities, and in particular championing the need to create effective software tools for academics.  A previous project, [Shuffl](https://code.google.com/p/shuffl/), conducted under a JISC Rapid Innovation program that he ran, trialled some early ideas that have contributed to the development of Annalist (since migrated to [GitHub](https://github.com/gklyne/shuffl/tree/master) and [GitHub wiki](https://github.com/gklyne/shuffl/blob/wiki/ProjectHome.md)). 
 
 More recently, work with the European [Wf4Ever project](http://www.wf4ever-project.org), EPSRC [Fusing Audio and Semantic Technologies (FAST)](http://www.semanticaudio.ac.uk) and Mellon [Cultures of Knowledge](http://www.culturesofknowledge.org) have provided valuable insights into the nature of tools needed to support publication of reproducible and re-usable research data.  Numerous experiments and discussions with colleagues have informed many of the design ideas and choices that have gone in to Annalist.
 

documents/TODO.md

@@ -62,7 +62,7 @@ See also: https://www.divio.com/en/blog/documentation/
 NOTE, for creating python3 virtual environment, use something like this:
 
     python3 -m venv anenv3
-    source anenv3/bin/activcate
+    source anenv3/bin/activate
     python -m pip install pip --upgrade
     python -m pip install --upgrade setuptools
 

documents/getting-started.md

@@ -60,6 +60,15 @@ In a working directory, and with Internet connection:
 
     python3 -m venv anenv3
     source anenv3/bin/activate
+    python -m pip install --upgrade pip
+    python -m pip install --upgrade certifi
+    python -m pip install --upgrade setuptools
+    pip install annalist
+
+Or, with Python 3.9:
+
+    /usr/local/bin/python3.9 -m venv --upgrade-deps anenv3
+    source anenv3/bin/activate
     pip install annalist
 
 ## Check the software installation, and initialize site data

documents/installing-annalist.md

@@ -72,16 +72,26 @@ The following assumes that software is installed under a directory called $WORKS
         cd $WORKSPACE
         python3 -m venv anenv3
         source anenv3/bin/activate
-        pip install --upgrade pip
-        pip install --upgrade certifi
+        python -m pip install --upgrade pip
+        python -m pip install --upgrade certifi
+        python -m pip install --upgrade setuptools
+        pip install annalist
+
+Or, with Python 3.9:
+
+        cd $WORKSPACE
+        /usr/local/bin/python3.9 -m venv --upgrade-deps anenv3
+        source anenv3/bin/activate
+        pip install annalist
+
 
 3.  Install the software from PyPI:
 
         pip install annalist
 
-4.  Alternatively, obtain a copy of the Annalist distribution kit, e.g. from [annalist.net](http://annalist.net/), and copy to a convenient location (e.g., $WORKSPACE/Annalist-0.5.16.tar.gz).  Then install it thus:
+4.  Alternatively, obtain a copy of the Annalist distribution kit, e.g. from [annalist.net](http://annalist.net/), and copy to a convenient location (e.g., $WORKSPACE/Annalist-0.5.18.tar.gz).  Then install it thus:
 
-        pip install $WORKSPACE/Annalist-0.5.16.tar.gz
+        pip install $WORKSPACE/Annalist-0.5.18.tar.gz
 
 5.  Finally, test the installed software:
 
@@ -90,27 +100,29 @@ The following assumes that software is installed under a directory called $WORKS
     The output from this command should look something like this:
 
         $ annalist-manager runtest
-        INFO:annalist_site.settings.runtests:Annalist version 0.5.16 (test configuration)
+        INFO:annalist_site.settings.runtests:Annalist version 0.5.18 (test configuration)
         INFO:annalist_site.settings.runtests:SETTINGS_MODULE:   annalist_site.settings.runtests
-        INFO:annalist_site.settings.runtests:BASE_DATA_DIR:     /Users/graham/workspace/github/gklyne/annalist/anenv2/lib/python2.7/site-packages/Annalist-0.5.16-py2.7.egg/annalist_root/sampledata/data
+        INFO:annalist_site.settings.runtests:BASE_DATA_DIR:     /Users/graham/workspace/github/gklyne/annalist/anenv3/lib/python3.9/site-packages/Annalist-0.5.18-py3.9.egg/annalist_root/sampledata/data
         INFO:annalist_site.settings.runtests:CONFIG_BASE:       /Users/graham/.annalist/
-        INFO:annalist_site.settings.runtests:DJANGO_ROOT:       /Users/graham/workspace/github/gklyne/annalist/anenv2/lib/python2.7/site-packages/django
-        INFO:annalist_site.settings.runtests:SITE_CONFIG_DIR:   /Users/graham/workspace/github/gklyne/annalist/anenv2/lib/python2.7/site-packages/Annalist-0.5.16-py2.7.egg/annalist_root/annalist_site
-        INFO:annalist_site.settings.runtests:SITE_SRC_ROOT:     /Users/graham/workspace/github/gklyne/annalist/anenv2/lib/python2.7/site-packages/Annalist-0.5.16-py2.7.egg/annalist_root
+        INFO:annalist_site.settings.runtests:DJANGO_ROOT:       /Users/graham/workspace/github/gklyne/annalist/anenv3/lib/python3.9/site-packages/django
+        INFO:annalist_site.settings.runtests:SITE_CONFIG_DIR:   /Users/graham/workspace/github/gklyne/annalist/anenv3/lib/python3.9/site-packages/Annalist-0.5.18-py3.9.egg/annalist_root/annalist_site
+        INFO:annalist_site.settings.runtests:SITE_SRC_ROOT:     /Users/graham/workspace/github/gklyne/annalist/anenv3/lib/python3.9/site-packages/Annalist-0.5.18-py3.9.egg/annalist_root
         INFO:annalist_site.settings.runtests:TEST_BASE_URI:     http://test.example.com/testsite
-        INFO:annalist_site.settings.runtests:DEFAULT_DB_PATH:   /Users/graham/workspace/github/gklyne/annalist/anenv2/lib/python2.7/site-packages/Annalist-0.5.16-py2.7.egg/annalist_root/sampledata/data/annalist_test/db.sqlite3
-        INFO:annalist_site.settings.runtests:DATABASE_PATH:     /Users/graham/workspace/github/gklyne/annalist/anenv2/lib/python2.7/site-packages/Annalist-0.5.16-py2.7.egg/annalist_root/sampledata/data/annalist_test/db.sqlite3
-        INFO:annalist_site.settings.runtests:STATICFILES_DIRS:  ((u'', u'/Users/graham/workspace/github/gklyne/annalist/anenv2/lib/python2.7/site-packages/Annalist-0.5.16-py2.7.egg/annalist_root/annalist/data/static'), (u'images', u'/Users/graham/workspace/github/gklyne/annalist/anenv2/lib/python2.7/site-packages/Annalist-0.5.16-py2.7.egg/annalist_root/annalist/data/identity_providers/images'))
-        INFO:annalist_site.settings.runtests:ANNALIST_LOG_PATH: /Users/graham/workspace/github/gklyne/annalist/anenv2/lib/python2.7/site-packages/Annalist-0.5.16-py2.7.egg/annalist_root/annalist.log
+        INFO:annalist_site.settings.runtests:DEFAULT_DB_PATH:   /Users/graham/workspace/github/gklyne/annalist/anenv3/lib/python3.9/site-packages/Annalist-0.5.18-py3.9.egg/annalist_root/sampledata/data/annalist_test/db.sqlite3
+        INFO:annalist_site.settings.runtests:DATABASE_PATH:     /Users/graham/workspace/github/gklyne/annalist/anenv3/lib/python3.9/site-packages/Annalist-0.5.18-py3.9.egg/annalist_root/sampledata/data/annalist_test/db.sqlite3
+        INFO:annalist_site.settings.runtests:STATICFILES_DIRS:  (('', '/Users/graham/workspace/github/gklyne/annalist/anenv3/lib/python3.9/site-packages/Annalist-0.5.18-py3.9.egg/annalist_root/annalist/data/static'), ('images', '/Users/graham/workspace/github/gklyne/annalist/anenv3/lib/python3.9/site-packages/Annalist-0.5.18-py3.9.egg/annalist_root/annalist/data/identity_providers/images'))
+        INFO:annalist_site.settings.runtests:ANNALIST_LOG_PATH: /Users/graham/workspace/github/gklyne/annalist/anenv3/lib/python3.9/site-packages/Annalist-0.5.18-py3.9.egg/annalist_root/annalist.log
+        Found 820 test(s).
         Creating test database for alias 'default'...
         System check identified no issues (0 silenced).
-        ...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
+        ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
         ----------------------------------------------------------------------
-        Ran 815 tests in 444.847s
+        Ran 820 tests in 193.291s
 
         OK
         Destroying test database for alias 'default'...
 
+
 For first-time installations, the Annalist site data will need to be initialized:  see section "Setting up an Annalist site" below.
 
 

documents/pages/index.html

@@ -15,8 +15,11 @@
   <div id="topheader">
     <h1 id="title">
       <a href="#">annalist.net</a> - 
-      <a htref="//demo.annalist.net/annalist/">Annalist</a> demonstration system
-      <span>0.5.16</span>
+      <a href="//annalist.net/annalist/">Annalist</a> demonstration system
+      <!--
+      <a href="//demo.annalist.net/annalist/">Annalist</a> demonstration system
+      -->
+      <span>0.5.18</span>
     </h1>
   </div>
   <!-- navigation -->
@@ -36,7 +39,7 @@ <h1 id="title">
   <h1>Welcome to annalist.net</h1>
 
   <p>
-    <a href="//demo.annalist.net/annalist/">Annalist demo server</a> (release 0.5.16).
+    <a href="//demo.annalist.net/annalist/">Annalist demo server</a> (release 0.5.18).
   </p>
 
   <h2>Overview</h2>
@@ -208,8 +211,11 @@ <h3>Software download</h3>
 
   <ul class="green">
     <li>
-      <a href="software/Annalist-0.5.16.tar.gz">Annalist-0.5.16</a>: 
-      Downloadable software installation kit.  Needs Python 2.7.15, <code>virtualenv</code> and <code>pip</code>.  Install using <code>pip</code> into a newly created Python virtual environment.  (Can also be used with Python 3.7 if dependencies are appropriately patched.)
+      <a href="software/Annalist-0.5.18.tar.gz">Annalist-0.5.18</a>: 
+      Downloadable software installation kit.  Needs Python 3.8 or 3.9, <code>virtualenv</code> and <code>pip</code>.  Install using <code>pip</code> into a newly created Python virtual environment.
+    </li>
+    <li>
+      <a href="software/Annalist-0.5.16.tar.gz">Annalist-0.5.16</a>  (older release).
     </li>
     <li>
       <a href="software/Annalist-0.5.14.tar.gz">Annalist-0.5.14</a>  (older release).