prepare for 1.14.2 release (changes.md)

Author: MathCancer

README.md

@@ -45,6 +45,8 @@ Visit http://MathCancer.org/blog for the latest tutorials and help.
       * rules-sample
       * physimess-sample
       * custom-division-sample
+      * asymmetric-division-sample
+      * immune-function-sample episode-sample
 
 **`make list-projects`** : list all available sample projects 
 
@@ -93,6 +95,8 @@ Version 1.14 upgrades the Cell Beheavior Hypothesis Grammar (to version 3), incl
 ### Version 1.14.2 (20 Jan 2025): 
 Version 1.14.2 primarily introduces bugfixes and stability refinements, closer matching to the cell behavior grammar (including the new `transition to X` synonym for `transform to X` behavior and better support for asymmetric division), a new script to more easily download PhysiCell Studio, and improvements to allow parallel "episodes" of PhysiCell in machine learning environments, such as the upcoming PhysiGym addon. 
 
+We are grateful for contributions by Vincent Noël, Randy Heiland, Daniel Bergman, Heber Rocha, and Elmar Bucher in this release. 
+
 ### Version 1.14.1 (13 Dec 2024): 
 Version 1.14.1 primarily introduces bug fixes as noted below, but also introduces the first implementation of asymmetric division. 
 

changes.md

@@ -5,6 +5,7 @@
 **Release dates:** 15 September 2024 - 
 * 1.14.0 : 15 September 2024
 * 1.14.1 : 13 December 2024
+* 1.14.2 : 20 January 2025
 
 ## Overview: 
 PhysiCell is a flexible open source framework for building agent-based multicellular models in 3-D tissue environments.
@@ -44,6 +45,8 @@ Visit http://MathCancer.org/blog for the latest tutorials and help.
       * rules-sample
       * physimess-sample
       * custom-division-sample
+      * asymmetric-division-sample
+      * immune-function-sample episode-sample
 
 **`make list-projects`** : list all available sample projects 
 
@@ -89,6 +92,11 @@ See changes.md for the full change log.
 ## Release summary: 
 Version 1.14 upgrades the Cell Beheavior Hypothesis Grammar (to version 3), including refinements to cell phagocytosis, effector attack, and cell damage/integrity in response to community discussions and peer review. It also introduces numerous refinements to cell division, random seeds, and randomized parameter initialization, as well as upgrades to PhysiBoSS and PhysiMeSS and bug fixes. Other refinements are "under the hood," including new GitHub actions and improved automation of testing, as well as improvements to MultiCellDS output. 
 
+### Version 1.14.2 (20 Jan 2025): 
+Version 1.14.2 primarily introduces bugfixes and stability refinements, closer matching to the cell behavior grammar (including the new `transition to X` synonym for `transform to X` behavior and better support for asymmetric division), a new script to more easily download PhysiCell Studio, and improvements to allow parallel "episodes" of PhysiCell in machine learning environments, such as the upcoming PhysiGym addon. 
+
+We are grateful for contributions by Vincent Noël, Randy Heiland, Daniel Bergman, Heber Rocha, and Elmar Bucher in this release. 
+
 ### Version 1.14.1 (13 Dec 2024): 
 Version 1.14.1 primarily introduces bug fixes as noted below, but also introduces the first implementation of asymmetric division. 
 
@@ -112,6 +120,9 @@ We are grateful for contributions by Vincent Noël, Randy Heiland, Daniel Bergma
 **NOTE 2:** Windows users need to follow an updated (from v1.8) MinGW64 installation procedure. This will install an updated version of g++, plus libraries that are needed for some of the intracellular models. See the [Setup Guides](https://github.com/physicell-training/ws2023/blob/main/agenda.md#set-up-physicell) for details.
 
 ### Major new features and changes in the 1.14.z versions
+#### 1.14.2
++ In anticipation with the upcoming `PhysiGym` addon (for machine learning / reinforcement learning), it is now possible to run multiple consecutive episodes from a single PhysiCell model within a runtime. The episode sample project demonstrates this possibility.
+ 
 #### 1.14.1 
 + asymmetric division is now possible through the config file
   + try the sample project with make `asymmetric-division-sample`
@@ -189,6 +200,31 @@ We are grateful for contributions by Vincent Noël, Randy Heiland, Daniel Bergma
   + set the svg substrate color function by default for config-only based implementation
 
 ### Minor new features and changes: 
+#### 1.14.2
+- [PR349](https://github.com/MathCancer/PhysiCell/pull/349) (minor improvement): `load_PhysiCell_config_file()` was split into `load_PhysiCell_config_file()` and `read_PhysiCell_config_file()` functions
+- [PR349](https://github.com/MathCancer/PhysiCell/pull/349) (minor improvement): `BioFVM BioFVM_microenvironment::initialize_microenvironment()` was split into `initialize_microenvironment()` and `set_microenvironment_initial_condition()` functions.
+- [PR349](https://github.com/MathCancer/PhysiCell/pull/349) (minor improvement): In `BioFVM/BioFVM_MultiCellDS.*`, a new `reset_BioFVM_substrates_initialized_in_dom()` function was added.
+- [PR349](https://github.com/MathCancer/PhysiCell/pull/349) (minor improvement): A new `BioFVM::BioFVM_basic_agent::reset_max_basic_agent_ID()` function was added. 
+- Switched `setup_cell_rules( void )` to output the full list of signals and behaviors with synonyms in `./output/dictionaries.txt` for fuller reference. 
+- Added new functions:
+  - `void display_signal_dictionary_with_synonyms( std::ostream& os )`
+  - `void display_response_dictionary_with_synonyms( std::ostream& os )`
+- Added `transition to X` and `transition to cell type N` as synonyms for the behavior `transform to X` (with synonym `transform to cell type X`), at the request of the cancer community who regard `transformation` as synonymous with `cancerous transformation`. (And `transition to X` is now the "primary" name for the behavior.) 
+- [PR352](https://github.com/MathCancer/PhysiCell/pull/352) (minor improvement): more robust macro to check for windows machines when creating directories
+- [PR353](https://github.com/MathCancer/PhysiCell/pull/353) (minor feature): Python script to download latest release of Studio (and create /studio).
+
+  To use it, go to the root directory and run:
+
+  ```
+  python beta/get_physicell.py
+  ```
+
+  and then to run studio (with the template project):
+
+  ```
+    make reset && make template && make
+    python studio/bin/studio.py & 
+  ```
 #### 1.14.1
 - PhysiBoSS PDFs removed from repo, links provided in tutorial README.md
 - build binaries on release `published` instead of `created`
@@ -204,6 +240,10 @@ We are grateful for contributions by Vincent Noël, Randy Heiland, Daniel Bergma
 + throw error if duplicate substrate or user_parameter name found
 
 ### Bugfixes: 
+#### 1.14.2 
++ [PR350](https://github.com/MathCancer/PhysiCell/pull/350) (minor fix): use standard save event triggers in asymmetric division example
++ [PR351](https://github.com/MathCancer/PhysiCell/pull/351) (minor fix): re-round template project cycle durations
+
 #### 1.14.1
 - store value of `attack_duration` when parsing config file
 - set rules to Version 3.0 for all projects