Changes

Summary

1. Initial version of Python plugin (#1085). (details)
2. Initial checkin of PythonQt plugin (#1086). (details)
3. Tidyup to Python plugin's configuration (#1085). (details)
4. Commit e115539 means we no longer have to undefine `UNICODE` (#1085). (details)
5. Rework Python build to allow us to use `find_package()` to get (details)
6. Python build can't use QT_KEYWORDS as the name `slots` is used in a (details)
7. Tidy up Python build process (#1085). (details)
8. Initialise/finalise the Python library in its plugin (#1085). (details)
9. Always build Python (until we setup the download of a pre-built system) (details)
10. Get Python and PythonQt building under Windows... (details)
11. Work on OpenSSL plugin (#1101). (details)
12. Specify branch of OpenSSL sub-module. (details)
13. Provide a mechanism to package and download pre-built libraries (#1106). (details)
14. Provide a sample plugin to demonstrate and test the use of packaged (details)
15. Use CHECK_FILES macro when retrieving binary files (#1106). (details)
16. Work on OpenSSL plugin (#1101). (details)
17. Use the `1_0_2h` release of OpenSSL (#1088 and #1101). (details)
18. Get example of packaging an external library working under Windows (details)
19. Don't duplicate `CHECKED_FILES` list when generating (details)
20. Get OpenSSL building under Windows (#1101). (details)
21. Windows OpenSSL 1.0.2h needs patching to build -- see (details)
22. gitignore directories containing pre-built packages (#1106). (details)
23. Clean up Python build and use new packaging macros (#1085). (details)
24. Work on the Python build system (#1085). (details)
25. Correctly initialise PYTHONHOME (#1085). (details)
26. General: some work on forcing plugins to reference one of the categories (details)
27. Work on using Cmake's ExternalProject module for third party builds. (details)
28. TEMP: build a minimal system to test ExternalProject. (details)
29. Fix typo. (details)
30. Work on zlib as ExternalProject for Windows. (details)
31. Add new parameters to ADD_PLUGIN for future improvements to handle (details)
32. Get ExternalProject build of zlib working under Windows. (details)
33. Re-enable full system build. (details)
34. Set @rpath on macOS libraries when they are copied into the application (details)
35. We no longer need to explicitly link to libz in the plugins that use the (details)
36. Keep the zlib source and build directories away from git. (details)
37. We don't need to specify CMAKE_CONFIGURATION_TYPES when building zlib. (details)
38. Correctly set the name of the zlib DLL. (details)
39. Tidy up code (#1106). (details)
40. Only create a package's archive after the package has been built (details)
41. Use correct path to archive when downloading (#1106). (details)
42. Use more meaningful variable names in helper code for package retrieval (details)
43. Package a prebuilt zlib package (#1106). (details)
44. Build and package zlib under Windows (#1106). (details)
45. Minor tidying up. (details)
46. Build and package zlib under Linux (#1106). (details)
47. Update SHA1 values for macos. (details)
48. Add comments describing zlib's build and packaging (#1106). (details)
49. Use top-level .gitignore to ignore any ./external subdirectory in a (details)
50. Disable SampleExternal plugin until it is updated as Travis build is (details)
51. Work on adding OpenSSL as a plugin (#1101). (details)
52. Work on OpenSSL as a plugin using ExternalProject(#1101). (details)
53. Merging left us with a duplicate run of install_name_tool (#1106). (details)
54. Improve package retrieval (#1106). (details)
55. Don't run UPDATE step in ExternalProject_Add (#1106). (details)
56. Don't run UPDATE step in ExternalProject_Add (#1106). (details)
57. OpenSSL now builds as an external library and plugin (#1101). (details)
58. Remove unused git submodules. (details)
59. Remove unused files following merge. (details)
60. Fix a bad merge. (details)
61. Tidy up code. (details)
62. Extend ADD_PLUGIN macro to optionally copy a directory into the (details)
63. Save the root directory of external packages in global variables so (details)
64. Build package Python as an ExternalProject (#1085). (details)
65. Plugins: some work towards preventing old plugins from crashing OpenCOR (details)
66. Implement "help" and "pip" commands and run Python when there's no (details)
67. Consistently use UPPERCASE for CMake commands (#1085). (details)
68. CLI plugin initialisation now works as expected (#1173). (details)
69. DEST_EXTERNAL_BINARIES_DIR is now set globally. (details)
70. Tidy up Python plugin build (#1085). (details)
71. Build and package Python Qt as an External Project (1085). (details)
72. Revert PMR Workspaces code. (details)
73. Work on a Python console window (#1085). (details)
74. The Python Qt sources are no longer in a git sub-module (#1085). (details)
75. Work on new PythonQtSupport plugin (#1085). (details)
76. Work on PythonQt support module (1085). (details)
77. Get ctkAbstractPythonManager building with Qt5 (#1085). (details)
78. Tidy up removal of Python Qt submodule (#1085). (details)
79. Use our EXPORT macros in CTK headers (#1085). (details)
80. Use CTK's AbstractPythonManger with Python Qt (#1085). (details)
81. Use CTK's console widget for our Python console window (#1085). (details)
82. Rename `PythonQt` plugin to `PythonQtAPI` to avoid name clashes with the (details)
83. Tidy up code (#1085). (details)
84. Fix typos... (#1085). (details)
85. Use pre-built version of Python Qt (#1085). (details)
86. Specify Python plugin's dependencies. (details)
87. Get matplotlib working under PythonQt (#1085). (details)
88. A PythonQt wrapper plugin for OpenCOR (#1085). (details)
89. Get and set command history in a CTK window (#1085). (details)
90. Save and restore Python command history between sessions (#1085). (details)
91. Cleanup PythonQt *before* finalising Python in CTK Manager (#1085). (details)
92. Check that we have a large enough data store and a valid solver before (details)
93. Upgrade zlib to version 1.2.11 (#1193). (details)
94. Use a `DataStoreArray` class to manage numeric arrays (#1085). (details)
95. Make data storage and simulation classes available to Python via (details)
96. Delete the correct PythonQt manager (#1085). (details)
97. Minor code tidy (#1085). (details)
98. Update OpenSSL to version 1.0.2j (#1113). (details)
99. Specify NumPy include directory even if not yet built (#1085). (details)
100. Correctly specify PythonQt library under Windows (#1085). (details)
101. Get NumPy include directory right... (#1085). (details)
102. Upgrade OpenSSL to version 1.0.2k (#1202). (details)
103. Remove unused CMake parameter (#1085). (details)
104. Python helper scripts need to be in git... (#1085). (details)
105. Always update, and hence configure and build, CMake external projects (details)
106. The Python and PythonQtAPI plugins need code for their interfaces... (details)
107. Let CMake know the location of our Python headers andf library (#1085). (details)
108. Get OpenSSL building under Linux (#1101). (details)
109. Tidy up Python plugin's CMake script (#1085). (details)
110. More work on building Python under Linux (#1085). (details)
111. Ensure the Python library is linked to the OpenCOR executable for Linux (details)
112. Include SQLite in Python build (for IPython and Jupyter) (#1085). (details)
113. Download latest versions of pre-built external packages (#1106). (details)
114. Add initial versions of README files for building Python related (details)
115. We need to explicitly specify the locations of headers and libraries of (details)
116. Linking Python into OpenCOR executable is only for Linux (#1085). (details)
117. Use relative RPATHs in python executable (#1085). (details)
118. Use a new git branch for Jupyter specific changes (#1085). (details)
119. Include SQLite in Python build for IPython and Jupyter. (details)
120. Work on a Jupyter kernel for OpenCOR (#1085). (details)
121. Zipping the python library was referencing the partly created archive... (details)
122. Console window requires Python wrapper plugin (#1085). (details)
123. Don't crash getting simulations if there's no single cell widget... (details)
124. Update `ctkAbstractPythonManager::executeFile` for Python 3 (#1085). (details)
125. Use our PythonQt branch (#1085). (details)
126. Minor tidy ups (#1085). (details)
127. Retrieve the correct package archive when git branches differ in their (details)
128. Jupyter notebook runs an OpenCOR kernel! (#1085). (details)
129. PythonQtAPI plugin doesn't use the Plugin interface so remove it (details)
130. Specify base directory for external projects (1106). (details)
131. We need to export wrapped classes for Windows (#1085). (details)
132. Windows needs to access wrapped classes (#1085). (details)
133. Tidy up CMake files (#1106). (details)
134. Set a plugin's build dependencies as part of ADD_PLUGIN (#1106). (details)
135. Use `TARGET` instead of `DEPENDENCY` to specify the target when creating (details)
136. Use appropriate quiet option for `make` on the different platforms (details)
137. Use correct OpenSSL library names in a Windows debug build (#1101). (details)
138. Tidy up CMake script (#1106). (details)
139. Update Windows builds of external packages (#1106). (details)
140. Newly built external project files weren't always copied (#1106). (details)
141. Get Python plugin running under Windows (#1085). (details)
142. Upgrade numpy to version 1.12.0 (#1085). (details)
143. Patch IPython kernel to work with PythonQt (#1085). (details)
144. A Jupyter kernel specification for OpenCOR (#1085). (details)
145. Update README (#1085). (details)
146. We were installing numpy twice... (#1085). (details)
147. Fix Linux build of Python plugin (#1085). (details)
148. OpenSSL is now in a plugin so no need to deploy system version (#1101). (details)
149. Test was reversed in commit 60dbe7b... (#1085). (details)
150. Copy and fixup external binaries *before* plugin build and link to the (details)
151. Build latest version under MacOS and Linux (#1085). (details)
152. Use new name for Python runtime library directory (#1085). (details)
153. Extend `COPY_FILE_TO_BUILD_DIR` to optionally specify if copy should be (details)
154. Find SQLite3 under Linux (#1085), (details)
155. Extend `COPY_FILE_TO_BUILD_DIR` to optionally specify if copy should be (details)
156. External libraries weren't being linked to targets under Linux... (details)
157. Update external package archives for linux (#1106). (details)
158. Use a custom target when copying external binaries in CMake (#1106). (details)
159. Window's CLI build needs to know about EventLoopInterface (#1085). (details)
160. Tidy up EventLoopInterface code (#1085). (details)
161. Remove debugging (#1085). (details)
162. Add dependency rules for copying OpenCOR.com in a Windows' build #1106). (details)
163. Install and use SQLite3 library under Windows (#1085). (details)
164. Bundle SQLite3 shared library with Python (#1085). (details)
165. Provide a user with scripts to install Python packages, etc. and remove (details)
166. Run a Python module using `OpenCOR -c Python::MODULE_NAME` (#1085). (details)
167. Set the location of our DLLs under Windows so that they are found (details)
168. Cleanly shutdown our Jupyter kernel (#1085). (details)
169. New OS/X Python binaries with Jupyter dependencies (#1085). (details)
170. Ensure other plugins can find and use the Python installed into OpenCOR (details)
171. Add `CentralWidget::localFileName()` to get the local file name of an (details)
172. Tidy code (#1086). (details)
173. Add `openSimulation()` and `openRemoteSimulation()` to OpenCOR's Python (details)
174. Return dictionaries of data store variables to Python and work on (details)
175. Fix issues with deleting and creating data store array variables (details)
176. Catch all exceptions that BioSignalML might throw. (details)
177. Suppress compile warnings when using Python's headers (#1085). (details)
178. Tidy up code (#1086). (details)
179. Throw an exception if we can't run a simulation from Python (#1087). (details)
180. Allow Python to get the size of a DataStoreVariable (#1086). (details)
181. Enable Python to access and modify a simulation's parameters (#1087). (details)
182. We need to specify OpenSSL libraries as well as ROOT_DIR to ensure CMake (details)
183. Allow Solver properties to be set from Python (#1270). (details)
184. Miscellaneous code tidy. (details)
185. Cleanup: Remove the `Single Cell` view sources from the Python branch... (details)
186. Cleanup: Remove unused sample plugin (#1206). (details)
187. Update Python build script for new packaging mechanism (#1106). (details)
188. Rename `Python` plugin to `PythonLibrary` (#1310). (details)
189. Fix bad merge into branch (#1306). (details)
190. Changed our license to GPL v3.0 (#1301). (details)
191. Pass full path as destination directory of an external package (#1106). (details)
192. Export Python version and site packages directory; tidy up CMake code (details)
193. Python package distributions don't always have binary files that require (details)
194. Bundle our Python packages in their own plugin (#1310). (details)
195. Revert commit dfbc536 as we use the SHA1_FILES to determine if a package (details)
196. Work on packaging of Python site packages (#1310). (details)
197. Tidy up code (#1310). (details)
198. Make sure Python executable can find libraries under OS/X (#1310). (details)
199. Update patch utility for Python 3 when debugging. (details)
200. Changed our license to GPL v3.0 (#1301). (details)
201. Update PythonQtAPI build script for new packaging mechanism (#1106). (details)
202. Use PythonQt's `qmake` based build (#1310). (details)
203. RETRIEVE_PACKAGE_FILE(): optionally allow a package's release tag and/or (details)
204. Specify PACKAGE_REPOSITORY and RELEASE_TAG for PythonQtAPI (#1306). (details)
205. Correctly reference PythonQt's include files (#1310). (details)
206. Rename `PythonLibrary` plugin back to `Python` (#1310). (details)
207. Python wrapper plugin uses Python packages plugin (#1310). (details)
208. Use `PACKAGE_NAME` in build scripts (#1306). (details)
209. Use `opencor/python` for prebuilt packages and wheels (#1310). (details)
210. PythonQt repository is now `pythonqt` (#1306). (details)
211. Fix typo (#1310). (details)
212. Work on an interface for wrapping classes to use with Python (#1275). (details)
213. Get `qmake` PythonQt build working on Linux (#1310). (details)
214. Tweaks and new binaries for PythonQt (#1306). (details)
215. New PythonQt binaries for Qt 5.9 (#1311). (details)
216. New Python binaries with runtime library sources bundled (#1310). (details)
217. PythonWrapper plugin has to have a CMake dependency on PythonPackages (details)
218. Use an IPython console for Python (#1324). (details)
219. We need to explicitly delete our IPython container window when (details)
220. Tidy up IPython widget creation code (#1324). (details)
221. Set the initial font size for our IPython window (#1324). (details)
222. The Python console window doesn't depend on OpenCOR's classes being (details)
223. Our mods to PythonQt mean we can revert to using method calls to get (details)
224. Redirect Python logging output to the console (#1324). (details)
225. Update PythonQt to version 3.2.0 (#1324). (details)
226. Upgrade matplotlib to version 2.0.2 (details)
227. Actually provide a patch file for matplotlib... (details)
228. Don't start a matplotlib exec() loop when running under PythonQt (details)
229. Tweaks for Windows build of Python libraries (#1085). (details)
230. Get IPython running under Windows (#1324). (details)
231. Upgrade numpy to version 1.13.0 (#1324). (details)
232. Upgrade IPython to version 6.1.0 (#1324). (details)
233. OAuth plugin sources were missing after merge (#1306). (details)
234. Remove unused `diff` files (#1324). (details)
235. Put CTK code used by PythonQtSupport plugin inside `./src` directory (details)
236. Known include directories are now implicitly added (#1306). (details)
237. Reinstate INCLUDE_DIRS parameter to specify additional include (details)
238. We do depend on the order that Python plugins are declared... (#1306). (details)
239. Suppress warning messages from compile (#1324). (details)
240. Correctly refer to the PythonQt library (#1324). (details)
241. Update binaries for Python packages and PythonQt (#1324). (details)
242. Python plugins need to be declared *after* other third-party plugins (details)
243. CMake: as a safeguard, make sure that empty variables are defined. (details)
244. PythonQt needs QtQuickWidgets library (#1086). (details)
245. Use an plugin interface for Python class wrapping (#1275). (details)
246. Tidy up code for calling a Python script (#1275). (details)
247. `INCLUDE_DIRS` parameter to `ADD_PLUGIN` is not needed if Python headers (details)
248. Minor tidy-up to comment. (details)
249. Tidying up. (details)
250. Export `${PROJECT_NAME}_EXTERNAL_SOURCES` so other plugins can use (details)
251. Resolve build issues with Python headers (#1376). (details)
252. Add missing `Simulation::fileName()`; fix name of include. (details)
253. Python: rename `PythonQtSupport` plugin to `PythonSupport`. (details)
254. Tidy code: use a better name for some `SimulationResults` methods. (details)
255. Optimisation: track indices of constants having gradients calculated. (details)
256. Optimisation: add sensitivity analysis to the CVode solver. (details)
257. Optimisation: tidy solver interface initialisation code. (details)
258. Optimisation: allocate array and data store to hold sensitivity (details)
259. Optimisation: use the sensitivity analysis solver. (details)
260. Optimisation: initialise array pointer... (details)
261. Optimisation: save gradient values and make available to Python. (details)
262. Python: a DataStore might not have a `voi`. (details)
263. Python: tidy simulation support wrapping code. (details)
264. Optimisation: gradients are of state variables wrt constant parameters. (details)
265. Optimisation: only store gradients if we have a gradients' data store... (details)
266. Optimisation: allow Python to set gradients' calculation flag and run (details)
267. Optimisation: default action is to calculate gradients. (details)
268. Optimisation: enable and use IDA sensitivity analysis. (details)
269. Optimisation: reinitialise CVode sensitivity analysis when (details)
270. Python: wait for a simulation to finish running before returning from (details)
271. Python: wait for a simulation to finish running before returning from (details)
272. Python: return result of simulation run. (details)
273. Optimisation: improve initialisation and error checking. (details)
274. WIP: track data store variable in a values dictionary. (details)
275. Python: dependencies of plugins using Python headers are on package (details)
276. Python: tweak name of PythonQt API build. (details)
277. Python: other plugins in fact depend on Python packages having been (details)
278. Python: don't check whether the memory associated with a simulation can (details)
279. Python: update packages for GCC 5.4 (#1391) (details)
280. Python: support plugin now needs to directly link to the Python plugin. (details)
281. Python: specify dependency for DataStore plugin. (details)
282. Python: update displayed values in simulation information widget when (details)
283. Python: allow for a DataStoreVariable not having a DataStoreArray (details)
284. Python: tidy code. (details)
285. DataStore: check we have a value's array before referencing it... (details)
286. Python: throw an error if there is an error when running a simulation. (details)
287. Python: throw an error if we are unable to open a simulation. (details)
288. Python: tidy code. (details)
289. Optimisation: use STAGGERED sensitivity analysis for IDAS (instead of (details)
290. Python: throw an exception when a simulation fails. (details)
291. Python: use full pathname of a file when initialising a simulation. (details)
292. Python: fix syntax error when non-debug build. (details)
293. Python: remove unused message. (details)
294. Optimisation: Add icon for `constant with gradient`. (details)
295. Python: clear simulation data when resetting a simulation. (details)
296. CVODE and IDA solver classes have been renamed. (details)
297. Python: Get clean build with MSVC 2014 Update 3. (details)
298. Python: Update pre-built packages for Windows. (details)
299. Python: get a clean build with MSVC 2014. (details)
300. Python: add typedef for std::bind result under gcc. (details)
301. Python: add typedef for std::bind result under gcc. (details)
302. Python: virtualenv-tools.py as downloaded from (details)
303. Python: rename utility to set_python_path.py (details)
304. Python: update Python path utility for for Python 3 and Windows and (details)
305. Python: install Windows Python package installers as scripts instead of (details)
306. Python: allow for spaces in path names. (details)
307. Python: use `argparse` and update help text. (details)
308. Python: package Python into Windows installer. (details)
309. Python: modify scripts to use the newly installed Python under Windows. (details)
310. Python: tweak command to set path to new Python executable. (details)
311. Python: add our Python script directory to the system PATH. (details)
312. Python: use a smaller font in IPython window. (details)
313. Python: update Python script paths in build directory. (details)
314. Python: Windows' package needs to include the SQLite3 import library. (details)
315. Python: add '.' to the head of IPython's search path. (details)
316. Python: remove `virtualenv` specific code. (details)
317. Python: turn off output when updating path to Python unless `--verbose` (details)
318. Python: update to IPython 6.2.1 and qtconsole 4.3.1 (details)
319. Python: update `PythonPackages` for WIndows and Linux. (details)
320. Python: cleaning up. (details)
321. Python: don't open remote files twice... (details)
322. Python: work on documentation. (details)
323. Python: don't include interface code when building WebKit libraries. (details)
324. Python: build Qt wrappers for WebKit. (details)
325. Python: tidy up code. (details)
326. Python: get our Web browser as a QWebView. (details)
327. Python: remove unused code. (details)
328. Python: rework console creation code. (details)
329. Python: new PythonQt library (with WebKit wrappers) for macos. (details)
330. SUNDIALS: upgraded to version 3.0.0 (#1453). (details)
331. Python: upgrade numpy to v1.13.3. (details)
332. Python: upgrade matplotlib to v2.1.0. (details)
333. Python: bundle lxml package (version 4.1.1). (details)
334. Python: use better names for `double *` arrays. (details)
335. Merge commit '76cd773' into pythonplugin (details)
336. Merge commit '2b65c99' into pythonplugin (details)
337. Python: fixes and tidy ups after merging. (details)
338. Use new style signal/slot connect() and tidy code. (details)
339. Python: let our simulation widget know a run is starting. (details)
340. Python: delete DataStoreArrays when their ref count reaches zero. (details)
341. Python: resetting parameters and clearing results are two different (details)
342. Python: delete gradients array before creating a new gradients data (details)
343. Python: tidy code. (details)
344. Python: fix bad merge. (details)
345. Data store: make sure arrays are initialised when allocated. (details)
346. Python: only build Python and PythonPackages plugin, with `sphinx` as (details)
347. Python: ignore sub-directories when updating Python runtime path in (details)
348. Python: don't apply patches for Windows when not building a Windows (details)
349. Python: update `pip`, `setuptools` and `wheel` to latest versions. (details)
350. Python: export ${PYTHON_RELATIVE_RUNTIME_DIR} to CMake. (details)
351. Python: script tidy up. (details)
352. Python: export ${SPHINX_BUILD_EXECUTABLE} to CMake. (details)
353. Converted CMake language commands and our macros to lower case. (details)
354. Python: ignore files we can't access when updating scripts. (details)
355. Python: define location of scripts. (details)
356. Python: build Sphinx package for Windows. (details)
357. Python: new release for Windows. (details)
358. Python: new release for Linux. (details)
359. Python: make sure our scripts don't access any local site-packages (details)
360. Python: update CLI tests for plugin. (details)
361. Tests: plugin status report includes `OpenSSL` and `zlib` so add them to (details)
362. Minor tidy. (details)
363. Python: remove/revert files not part of bundling runtime. (details)
364. Python: remove more unneeded files. (details)
365. Python: more tidying up. (details)
366. Some minor cleaning up for our main CMakeLists.txt file (#1607). (details)
367. Some minor cleaning up for our main CMakeLists.txt file (#1607). (details)
368. Some minor cleaning up. (details)
369. Some minor cleaning up for our main CMakeLists.txt file (#1607). (details)
370. Some minor cleaning up for our main CMakeLists.txt file (#1607). (details)
371. Some minor cleaning up for our main CMakeLists.txt file (#1607). (details)
372. Slight update to our make/common.cmake file. (details)
373. Some minor cleaning up for our pythonplugin.* and pythonpackagesplugin.* (details)
374. Some minor cleaning up for our pythonplugin.* and pythonpackagesplugin.* (details)
375. Python: don't actually deploy any code. (details)
376. Python: PythonPackages build depends on a built Python. (details)
377. Python: don't include plugin libraries with OpenCOR. (details)
378. Python: use a global target, OpenCORBuild, to ensure Python plugin (details)
379. Python: also use Release build for Debug under Windows. (details)
380. Python: new PythonPackages for macOS and Linux. (details)
381. Python: tweak CMake targets and dependencies. (details)
382. Python: Windows debug mode packages. (details)
383. Python: update tests since Python is no longer a deployed plugin. (details)
384. Python: minor tweaks. (details)
385. Python: remove unused script. (details)
386. Some minor cleaning up. (details)
387. Removed the "Constant with gradient" icon, which we don't use yet. (details)
388. Some minor cleaning up. (details)
389. Some minor cleaning up. (details)
390. Temporarily build the Python and PythonPackages plugins. (details)
391. Some minor cleaning up. (details)
392. Some minor cleaning up. (details)
393. Temporarily build the OpenSSL, Python, PythonPackages and zlib plugins (details)
394. Some minor cleaning up. (details)
395. Some minor cleaning up. (details)
396. Some minor cleaning up. (details)
397. Some minor cleaning up. (details)
398. Some minor cleaning up. (details)
399. Rebuild a default version of OpenCOR. (details)
400. Revert "Rebuild a default version of OpenCOR." (details)
401. Some minor cleaning up. (details)
402. Rebuild a default version of OpenCOR. (details)

Initial version of Python plugin (#1085).

Initial checkin of PythonQt plugin (#1086).

Tidyup to Python plugin's configuration (#1085).

Commit e115539 means we no longer have to undefine `UNICODE` (#1085).

Rework Python build to allow us to use `find_package()` to get
configuration (#1085).

Python build can't use QT_KEYWORDS as the name `slots` is used in a
header file (#1085).

Tidy up Python build process (#1085).

Initialise/finalise the Python library in its plugin (#1085).

Always build Python (until we setup the download of a pre-built system)
and exclude the built files from git (#1085).

Get Python and PythonQt building under Windows...

Work on OpenSSL plugin (#1101).

Specify branch of OpenSSL sub-module.

Provide a mechanism to package and download pre-built libraries (#1106).

Provide a sample plugin to demonstrate and test the use of packaged
pre-built libraries (#1106).

Use CHECK_FILES macro when retrieving binary files (#1106).

Work on OpenSSL plugin (#1101).
Use new packaging system for OpenSSL libraries; cleanup paths in OS/X
libraries; use OpenSSL 1.0.2 because libgit2 doesn't like 1.1.0. 

Use the `1_0_2h` release of OpenSSL (#1088 and #1101).

Get example of packaging an external library working under Windows
(#1106).

Don't duplicate `CHECKED_FILES` list when generating
`RETRIEVE_PACKAGE_FILE` code (#1106).

Get OpenSSL building under Windows (#1101).

Windows OpenSSL 1.0.2h needs patching to build -- see
https://github.com/openssl/openssl/issues/1545 (#1101).

gitignore directories containing pre-built packages (#1106).

Clean up Python build and use new packaging macros (#1085).

Work on the Python build system (#1085).

Correctly initialise PYTHONHOME (#1085).
This allows the shell to find Python libraries bundled with OpenCOR.

General: some work on forcing plugins to reference one of the categories
we support (#1111).

Work on using Cmake's ExternalProject module for third party builds.

TEMP: build a minimal system to test ExternalProject.

Fix typo.

Work on zlib as ExternalProject for Windows.

Add new parameters to ADD_PLUGIN for future improvements to handle
EXTERNAL packages.

Get ExternalProject build of zlib working under Windows.

Re-enable full system build.

Set @rpath on macOS libraries when they are copied into the application
bundle so that we no longer have to set it in objects that link the
library (#1159).

We no longer need to explicitly link to libz in the plugins that use the
libzlib plugin.

Keep the zlib source and build directories away from git.

We don't need to specify CMAKE_CONFIGURATION_TYPES when building zlib.

Correctly set the name of the zlib DLL.

Tidy up code (#1106).

Only create a package's archive after the package has been built
(#1106).

Use correct path to archive when downloading (#1106).

Use more meaningful variable names in helper code for package retrieval
(#1106).

Package a prebuilt zlib package (#1106).

Build and package zlib under Windows (#1106).

Minor tidying up.

Build and package zlib under Linux (#1106).

Update SHA1 values for macos.

Add comments describing zlib's build and packaging (#1106).

Use top-level .gitignore to ignore any ./external subdirectory in a
plugin's directory (#1106).

Disable SampleExternal plugin until it is updated as Travis build is
failing (PR #1162).

Work on adding OpenSSL as a plugin (#1101).

Work on OpenSSL as a plugin using ExternalProject(#1101).

Merging left us with a duplicate run of install_name_tool (#1106).

Improve package retrieval (#1106).
Use `PACKAGE_VERSION` to refer to a package's version when generating
retrieval code; check that we have the expected number and order of
arguments when retrieving a package.

Don't run UPDATE step in ExternalProject_Add (#1106).
We are building against a tagged release and re-running update triggers
build/configure/install steps...

Don't run UPDATE step in ExternalProject_Add (#1106).

OpenSSL now builds as an external library and plugin (#1101).

Remove unused git submodules.

Remove unused files following merge.

Fix a bad merge.

Tidy up code.

Extend ADD_PLUGIN macro to optionally copy a directory into the
generated application (#1106).

Save the root directory of external packages in global variables so
CMake can find them when building other packages (#1161).

Build package Python as an ExternalProject (#1085).

Plugins: some work towards preventing old plugins from crashing OpenCOR
(#1163).

Implement "help" and "pip" commands and run Python when there's no
command (#1085).

Consistently use UPPERCASE for CMake commands (#1085).

CLI plugin initialisation now works as expected (#1173).

DEST_EXTERNAL_BINARIES_DIR is now set globally.

Tidy up Python plugin build (#1085).

Build and package Python Qt as an External Project (1085).

Revert PMR Workspaces code.

Work on a Python console window (#1085).
These files are copied from the Common Toolkit (CTK) project
(https://github.com/commontk/CTK) as of commit 04607d0.

The Python Qt sources are no longer in a git sub-module (#1085).

Work on new PythonQtSupport plugin (#1085).

Work on PythonQt support module (1085).
Use CTK's Python manager for Python Qt.

Get ctkAbstractPythonManager building with Qt5 (#1085).

Tidy up removal of Python Qt submodule (#1085).

Use our EXPORT macros in CTK headers (#1085).

Use CTK's AbstractPythonManger with Python Qt (#1085).

Use CTK's console widget for our Python console window (#1085).

Rename `PythonQt` plugin to `PythonQtAPI` to avoid name clashes with the
actual Python Qt library (#1085).

Tidy up code (#1085).

Fix typos... (#1085).

Use pre-built version of Python Qt (#1085).

Specify Python plugin's dependencies.

Get matplotlib working under PythonQt (#1085).

A PythonQt wrapper plugin for OpenCOR (#1085).

Get and set command history in a CTK window (#1085).

Save and restore Python command history between sessions (#1085).

Cleanup PythonQt *before* finalising Python in CTK Manager (#1085).

Check that we have a large enough data store and a valid solver before
starting a simulation (#1200).

Upgrade zlib to version 1.2.11 (#1193).

Use a `DataStoreArray` class to manage numeric arrays (#1085).

Make data storage and simulation classes available to Python via
PythonQt wrappers (#1085).
This requires wrapped classes to be QObjects with wrapped methods
exposed as public slots and class names specified in full.

Delete the correct PythonQt manager (#1085).

Minor code tidy (#1085).

Update OpenSSL to version 1.0.2j (#1113).

Specify NumPy include directory even if not yet built (#1085).

Correctly specify PythonQt library under Windows (#1085).

Get NumPy include directory right... (#1085).

Upgrade OpenSSL to version 1.0.2k (#1202).

Remove unused CMake parameter (#1085).

Python helper scripts need to be in git... (#1085).

Always update, and hence configure and build, CMake external projects
(#1106).

The Python and PythonQtAPI plugins need code for their interfaces...
(#1085).

Let CMake know the location of our Python headers andf library (#1085).

Get OpenSSL building under Linux (#1101).

Tidy up Python plugin's CMake script (#1085).

More work on building Python under Linux (#1085).

Ensure the Python library is linked to the OpenCOR executable for Linux
(#1085).

Include SQLite in Python build (for IPython and Jupyter) (#1085).

Download latest versions of pre-built external packages (#1106).

Add initial versions of README files for building Python related
plugins.

We need to explicitly specify the locations of headers and libraries of
pre-built external projects (#1106).

Linking Python into OpenCOR executable is only for Linux (#1085).

Use relative RPATHs in python executable (#1085).

Use a new git branch for Jupyter specific changes (#1085).

Include SQLite in Python build for IPython and Jupyter.

Work on a Jupyter kernel for OpenCOR (#1085).

Zipping the python library was referencing the partly created archive...
(#1085).

Console window requires Python wrapper plugin (#1085).

Don't crash getting simulations if there's no single cell widget...
(#1085)

Update `ctkAbstractPythonManager::executeFile` for Python 3 (#1085).

Use our PythonQt branch (#1085).

Minor tidy ups (#1085).

Retrieve the correct package archive when git branches differ in their
package configuration and/or version (#1106).

Jupyter notebook runs an OpenCOR kernel! (#1085).

PythonQtAPI plugin doesn't use the Plugin interface so remove it
(#1085).

Specify base directory for external projects (1106).
This helps prevent path names becoming too long during Windows' builds.

We need to export wrapped classes for Windows (#1085).

Windows needs to access wrapped classes (#1085).

Tidy up CMake files (#1106).

Set a plugin's build dependencies as part of ADD_PLUGIN (#1106).

Use `TARGET` instead of `DEPENDENCY` to specify the target when creating
a package (#1106).

Use appropriate quiet option for `make` on the different platforms
(#1101).

Use correct OpenSSL library names in a Windows debug build (#1101).

Tidy up CMake script (#1106).

Update Windows builds of external packages (#1106).

Newly built external project files weren't always copied (#1106).
Only do a direct copy if the file exists and the plugin doesn't depend
on any targets.

Get Python plugin running under Windows (#1085).
Also tidy up CMake code.

Upgrade numpy to version 1.12.0 (#1085).

Patch IPython kernel to work with PythonQt (#1085).

A Jupyter kernel specification for OpenCOR (#1085).

Update README (#1085).

We were installing numpy twice... (#1085).

Fix Linux build of Python plugin (#1085).

OpenSSL is now in a plugin so no need to deploy system version (#1101).

Test was reversed in commit 60dbe7b... (#1085).

Copy and fixup external binaries *before* plugin build and link to the
destination copy (#1106).

Build latest version under MacOS and Linux (#1085).

Use new name for Python runtime library directory (#1085).

Extend `COPY_FILE_TO_BUILD_DIR` to optionally specify if copy should be
before the target is built (#1106).

Find SQLite3 under Linux (#1085),

Extend `COPY_FILE_TO_BUILD_DIR` to optionally specify if copy should be
before the target is built (#1106).

External libraries weren't being linked to targets under Linux...
(#1106).

Update external package archives for linux (#1106).

Use a custom target when copying external binaries in CMake (#1106).

Window's CLI build needs to know about EventLoopInterface (#1085).

Tidy up EventLoopInterface code (#1085).

Remove debugging (#1085).

Add dependency rules for copying OpenCOR.com in a Windows' build #1106).

Install and use SQLite3 library under Windows (#1085).

Bundle SQLite3 shared library with Python (#1085).

Provide a user with scripts to install Python packages, etc. and remove
`pip` as a plugin command (#1085).
If we run pip as `OpenCOR -c Python::pip` then pip tries to run OpenCOR
as a sub-process rather than the Python that started pip.

Run a Python module using `OpenCOR -c Python::MODULE_NAME` (#1085).

Set the location of our DLLs under Windows so that they are found
(#1085).

Cleanly shutdown our Jupyter kernel (#1085).

New OS/X Python binaries with Jupyter dependencies (#1085).

Ensure other plugins can find and use the Python installed into OpenCOR
(#1085).

Add `CentralWidget::localFileName()` to get the local file name of an
open remote url.

Tidy code (#1086).

Add `openSimulation()` and `openRemoteSimulation()` to OpenCOR's Python
module (#1086).

Return dictionaries of data store variables to Python and work on
allowing Python code to set parameter values (#1086).

Fix issues with deleting and creating data store array variables
(#1086).

Catch all exceptions that BioSignalML might throw.

Suppress compile warnings when using Python's headers (#1085).

Tidy up code (#1086).

Throw an exception if we can't run a simulation from Python (#1087).

Allow Python to get the size of a DataStoreVariable (#1086).

Enable Python to access and modify a simulation's parameters (#1087).

We need to specify OpenSSL libraries as well as ROOT_DIR to ensure CMake
finds them (#1106).

Allow Solver properties to be set from Python (#1270).

Miscellaneous code tidy.

Cleanup: Remove the `Single Cell` view sources from the Python branch...
(#1256).