pct-code · teauxfu · Jun 4, 2021 · May 11, 2021 · May 13, 2021 · May 13, 2021
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,20 +4,33 @@ repos:
     hooks:
       - id: isort
         args: ["--profile", "black", "--filter-files"]
+
   - repo: https://github.com/ambv/black
     rev: 21.4b2
     hooks:
       - id: black
+
   - repo: https://gitlab.com/pycqa/flake8
     rev: 3.9.1
     hooks:
       - id: flake8
         args: ["--ignore=ANN001,ANN101,ANN002,W503", --max-line-length=88]
         additional_dependencies:
           - flake8-annotations
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v3.4.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: debug-statements
+
+  - repo: local
+    hooks:
+      - id: export-requirements
+        name: export-requirements
+        entry: poetry export
+        language: system
+        always_run: true
+        pass_filenames: false
+        args: ["-f", "requirements.txt", "--output", "requirements.txt"]
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,12 +1,57 @@
+=========
 Changelog
 =========
 
 All notable changes to this project will be documented in this file.
 
 The format is based on `Keep a
-Changelog <https://keepachangelog.com/en/1.0.0/>`__, and this project
+Changelog <https://keepachangelog.com/en/1.0.0/>`_, and this project
 adheres to `Semantic
-Versioning <https://semver.org/spec/v2.0.0.html>`__.
+Versioning <https://semver.org/spec/v2.0.0.html>`_.
+
+
+[v0.5.7]
+--------
+
+Changed
+~~~~~~~
+
+User experience
+===============
+
+- overhaul the :code:`TestHandlerView` to be better oragnized
+- overhaul the :code:`EvaluationWindow` to be better oragnized
+- setting labels for each :code:`Test` is now handled in the :code:`EvaluationWindow`s' "Plot" tab
+- updated docs
+- ensured exported plot dimensions are always uniform
+
+Performance
+===========
+
+- updated the :code:`TestHandler` to poll for readings asynchronously
+- updated the :code:`TestHandler` to be more robust when generating log files
+- minor performance buff to log processing
+- minor performance buff to the :code:`LivePlot` component
+- minor performance buff to :code:`Project` serialization
+- minor performance buff to reading user configuration file
+
+Data handling
+=============
+
+- the :code:`Project` data model now records calcium concentration
+- updated the :code:`Test` object model to handle the :code:`Reading` class
+- updated the :code:`Project` object model to be more backwards compatible
+- refactored data analysis out of the :code:`EvaluationWindow` and into its own :code:`score` function
+- updated :code:`score` function to handle the :code:`Reading` class
+
+Misc
+====
+
+- update all :code:`os.path` operations to fancy :code:`pathlib.Path` operations
+- update all :code:`matplotlib` code to use the object oriented API
+- fixed some lag that would accumulate when displaying log messages in the main menu
+- lots of misc. code cleanup / reorganizing
+
 
 [v0.5.6]
 --------
@@ -129,7 +174,7 @@ Added
 - report export as CSV (default)
 - report export as flattened JSON (not human readable)
 - more descriptive window titles, all windows get the app icon ###
- 
+
 Changed
 ~~~~~~~
 
@@ -143,7 +188,7 @@ Changed
 - general linting and cleanup ### Fixed
 - bug in observed baseline pressure reporting
 - the Live Plot stops updating (clearing itself) at the end of a test
- 
+
 Removed
 ~~~~~~~
 
@@ -159,6 +204,9 @@ Added
 
 - rinse dialog, accessible from the menu bar
 - help text, accessible from the menu bar
-- get\_resource function for getting resource files. can be used for resources with bundled executables later ### Changed
+- get_resource function for getting resource files. can be used for resources with bundled executables later
+
+Changed
+~~~~~~~
 - reset versioning to v0.1.0
 - moved project loading functionality to menu bar
diff --git a/COPYING b/COPYING
@@ -671,4 +671,4 @@ into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
-<https://www.gnu.org/licenses/why-not-lgpl.html>.
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
diff --git a/README.rst b/README.rst
@@ -9,9 +9,9 @@ performance testing.
 If you are working with Teledyne SSI Next Generation pumps generally, please check out `py-hplc`_!
 
 This project is stable and usable in a production environment, but listed as in beta due to the lack of a test suite (yet!).
-If you notice something weird, fragile, or otherwise encounter a bug, please open an `issue`_. 
+If you notice something weird, fragile, or otherwise encounter a bug, please open an `issue`_.
 
-.. image:: https://raw.githubusercontent.com/teauxfu/scalewiz/main/img/main_menu(details).PNG
+.. image:: https://raw.githubusercontent.com/teauxfu/scalewiz/main/img/main_menu.PNG
 
 .. image:: https://raw.githubusercontent.com/teauxfu/scalewiz/main/img/evaluation(plot).PNG
 
@@ -22,13 +22,22 @@ Installation
 
     python -m pip install --user scalewiz
 
+Or, if you use :code:`pipx` (`try it!`_ 😉) ::
+
+    pipx install scalewiz
+
 Usage
 =====
 
 ::
 
     python -m scalewiz
 
+If Python is on your PATH (or you used :code:`pipx` 😎), simply ::
+
+    scalewiz
+
+
 Further instructions can be viewed in the `docs`_ section of this repo or with the Help button in the main
 menu.
 
@@ -70,3 +79,4 @@ Acknowledgements
 .. _`py-hplc`: https://github.com/teauxfu/py-hplc
 .. _`docs`: https://github.com/teauxfu/scalewiz/blob/main/doc/index.rst#scalewiz-user-guide
 .. _`issue`: https://github.com/teauxfu/scalewiz/issues
+.. _`try it!`: https://pypa.github.io/pipx/
diff --git a/doc/index.rst b/doc/index.rst
@@ -30,7 +30,7 @@ If you need to clear a date field, just click its label.
 Experiment parameters
 ~~~~~~~~~~~~~~~~~~~~~
 
-This is the most important one. The first two fields only affect the
+This is the most important one. The first few fields only affect the
 final report. The last five fields affect how the tests are conducted
 and scored.
 
@@ -73,7 +73,7 @@ If you don't already have a project loaded, click 'Project' > 'Load
 existing' from the menu bar. If a project is currently loaded, it's name
 will be displayed as shown below.
 
-.. image:: ../img/main_menu(loaded).PNG
+.. image:: ../img/main_menu.PNG
    :alt: main menu with loaded project
 
 Use the 'Devices' dropdown boxes to select the serial ports the pumps
@@ -87,7 +87,10 @@ Blanks
 ~~~~~~
 
 If you are running a blank, enter a name for it. The notes field may be
-used to store any other relevant information. |trial entry|
+used to store any other relevant information.
+
+ .. image:: ../img/main_menu(blank).PNG
+    :alt: blank entry
 
 Trials
 ~~~~~~
@@ -113,13 +116,6 @@ You can interrupt the uptake cycle (or the test itself) at any time by
 clicking the 'Stop' button. This will stop the pumps, then attempt to
 save the data to file.
 
-While a test is running, you may click 'Toggle Details' to show/hide a
-more detailed view of the experiment state, including a live plot of the
-data as it is collected.
-
-.. image:: ../img/main_menu(details).PNG
-   :alt: live plot
-
 A test will automatically stop itself and the pumps when either the time
 limit or pressure limit has been reached. The 'Start' button will become
 a 'New' button, which you can use to initialize a new test.
@@ -130,9 +126,11 @@ Rinses
 Between each test, it is necessary to rinse the system. Clicking 'Rinse'
 from the menu bar will create a small dialog that can do this for you.
 
-|rinse dialog|
+.. image:: ../img/rinse_dialog.PNG
+   :alt: rinse dialog
 
-|rinse dialog in progress|
+.. image:: ../img/rinse_dialog(rinsing).PNG
+   :alt: rinse dialog in progress
 
 The button will temporarily disable while acting as a status label to
 show the progression of the rinse. Closing the dialog will terminate the
@@ -149,23 +147,25 @@ Click 'Evaluation' from the menu bar to open the Evalutaion Window.
 The data for each test in the project will be displayed horizontally as
 a row.
 
--  Report As: what to call the test on the plot
--  Minutes: the duration of the test, (# of measurements)
+-  Minutes: the duration of the test
 -  Pump: which series of pressure measurements to use for scoring
--  Baseline: the observed baseline pressure for the selected Pump
--  Max: the highest pressure observed for the selected Pump
+-  Baseline PSI: the observed baseline pressure for the selected Pump
+-  Max PSI: the highest pressure observed for the selected Pump
 -  Clarity: the observed water clarity
--  Notes: any misc. info associated with the test. may be edited at any
-   time
--  Result: the test's score, considering the selected Pump
--  Report: a checkbox for indicating whether or not a test should be
-   included on the report
+-  Notes: any misc. info associated with the test.
+-  Result: the test's score, considering the selected Pump and blanks on report
+-  Report: a checkbox for indicating whether or not a test should be included on the report
+
+.. note::
+
+   Blanks will only be factored into the scoring process if marked as 'On Report'
+
 
 Plot
 ~~~~
 
-The 'Plot' tab displays the most recent plot of all tests with a ticked
-'Include on Report' box.
+The 'Plot' tab displays the most recent plot of all tests with a ticked 'Include on Report' box.
+You can change the Label associated with each test using the entries on the right.
 
 .. image:: ../img/evaluation(plot).PNG
    :alt: plot frame with some data
@@ -178,10 +178,25 @@ The 'Calculations' tab displays a text log of the evaluation of all
 tests with a ticked 'Include on Report' box. This log is automatically
 exported next to the report file when you click the 'Export' button.
 
+.. image:: ../img/evaluation(calcs).PNG
+   :alt: calculations frame with some data
+
 Generating a report
 ~~~~~~~~~~~~~~~~~~~
 
 You can export a report at any time by clicking the 'Export' button.
+This will output, next to the Project's .json file,
+
+- a .txt file copy of the most recent calculations log
+- a .jpeg file of the Project's plot
+- an either .csv or .json file with a summary of the results
+
+.. note::
+
+   The results are typically exported to CSV for easier parsing in Excel or similar.
+   Support for JSON reports are more or less accidental at time of writing.
+   If you are able and or willing to parse the JSON, it may be more useful to just work with the Project's JSON file directly.
+
 
 Running tests concurrently
 --------------------------
@@ -193,9 +208,4 @@ tab will appear on the main menu, and can be used normally.
    :alt: two systems
 
 At the time of writing, a particular project may only be loaded to one
-system at a time. Loading the same project to more than one system may
-result in data loss.
-
-.. |trial entry| image:: ../img/main_menu(blank).PNG
-.. |rinse dialog| image:: ../img/rinse_dialog.PNG
-.. |rinse dialog in progress| image:: ../img/rinse_dialog(rinsing).PNG
+'System' at a time.
diff --git a/img/evaluation(calcs).PNG b/img/evaluation(calcs).PNG
diff --git a/img/evaluation(data).PNG b/img/evaluation(data).PNG
diff --git a/img/evaluation(plot).PNG b/img/evaluation(plot).PNG
diff --git a/img/main_menu(blank).PNG b/img/main_menu(blank).PNG
diff --git a/img/main_menu(concurrent).PNG b/img/main_menu(concurrent).PNG
diff --git a/img/main_menu(details).PNG b/img/main_menu(details).PNG
diff --git a/img/main_menu(loaded).PNG b/img/main_menu(loaded).PNG
diff --git a/img/main_menu(project).PNG b/img/main_menu(project).PNG
diff --git a/img/main_menu(running).PNG b/img/main_menu(running).PNG
diff --git a/img/main_menu(trial).PNG b/img/main_menu(trial).PNG
diff --git a/img/main_menu(uptake).PNG b/img/main_menu(uptake).PNG
diff --git a/img/main_menu.PNG b/img/main_menu.PNG
diff --git a/img/project_editor(experiment).PNG b/img/project_editor(experiment).PNG
diff --git a/img/project_editor(report).PNG b/img/project_editor(report).PNG
diff --git a/img/project_editor.PNG b/img/project_editor.PNG