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Bump version to v0.5.1
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Signed-off-by: Emanuel Lima <emanuel-lima@outlook.com>
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# Changelog:

### 0.5.0 - December 18 2023
## 0.5.1 - December 21, 2023

#### New User Features
### Bugs fixed

- Fixed a bug where the single_proc mode would result in a missing simulation key ([#332](https://github.com/cadCAD-org/cadCAD/issues/332));
- Fixed a bug where the single_proc mode would not return results ([#335](https://github.com/cadCAD-org/cadCAD/issues/335));
- Fixed a wrong parameter order when doing single runs ([#337](https://github.com/cadCAD-org/cadCAD/issues/337)).
- Added a Windows CI pipeline;

## 0.5.0 - December 20, 2023

### New User Features

- Added toggle for enabling users to deactivate deepcopying. This is done by passing an additional object on the `ExecutionContext`, eg. `ExecutionContext(mode, additional_objs={'deepcopy_off': True})`

#### New Submodules
### New Submodules

- A collection of type annotations for encapsuling `cadCAD` projects is now implemented through the `cadCAD.types` submodules
- Added `cadCAD.tools` as a submodule, which is originated from the `cadCAD_tools` Python package. This submodule contains several helper functions for making the simulation experience more straightforward as well as a collection of performance profiling tools.
- Added `cadCAD.diagram` as a submodule, which is originated from the `cadCAD_diagram` Python package. This submodule contains functions for programatically generating block diagrams from existing models.
- More informative error messages when policies and SUFs are wrongly implemented. (Issues #288 and #258)

#### Backend Improvements
### Backend Improvements

- Merged repo with the `cadCAD_legacy_devel`, which includes performance improvements. In particular, simulations will start up faster due to code optimizations.
- `cadCAD` now uses `pytest` as the testing framework. This was made possible by isolating the existing tests and wrapping them into functions.
- `cadCAD` now uses `pytest` as the testing framework. This was made possible by isolating the existing tests and wrapping them into functions.

#### Fixes
### Fixes

- cadCAD is now Python 3.10+ compatible (Issue #306 and #301)
- Proper support for `ExecutionMode.single_mode` (Issue #253 and #254)

### September 28, 2021
#### New Features:
## September 28, 2021
### New Features:
* **ver. ≥ `0.4.28`:**
* ##### [Experiments](documentation#experiments)
* ##### System Model Configuration
* #### [Experiments](documentation#experiments)
* #### System Model Configuration
* Configurations (`cadCAD.utils.Configuration`'s) are now accessed via the `configs` member of `cadCAD.configuration.Experiment`.
[Example:](documentation#experiments) `cadCAD.configuration.Experiment().configs`
* `cadCAD.configs` has been re-included for backwards compatibility and has been assigned `cadCAD.experiment.configs`
* ##### Experiments
* `cadCAD.configuration.Experiment()` is unique representation of an experiment of one or more configured System
* #### Experiments
* `cadCAD.configuration.Experiment()` is unique representation of an experiment of one or more configured System
Models.
* The `cadCAD` module now contains a default Experiment object `cadCAD.experiment` as an instantiation of
* The `cadCAD` module now contains a default Experiment object `cadCAD.experiment` as an instantiation of
`cadCAD.configuration.Experiment()`
* An `Experiment`'s `append_model` method stores multiple system model `Configuration`'s for simulation
* An `Experiment`'s `append_model` method stores multiple system model `Configuration`'s for simulation
execution within `cadCAD.configuration.Experiment().configs`.
`cadCAD.configuration.Experiment().model_ids` contains system model labels and/or indexes for
`cadCAD.configuration.Experiment().model_ids` contains system model labels and/or indexes for
`cadCAD.configuration.Experiment().configs`
* The `Experiment`'s `append_model` method is defined with `model_id` parameter that accepts a system model
* The `Experiment`'s `append_model` method is defined with `model_id` parameter that accepts a system model
label.
* If duplicate `model_id`'s are specified, an index is appended to the label after the `@` symbol.
(Example: `cadCAD.configuration.Experiment().model_ids = ['sys_model', 'sys_model@1', 'sys_model@2', ...]`)
* If `model_id`'s are not specified or duplicate, the label is auto-generated as a string indicating the
(Example: `cadCAD.configuration.Experiment().model_ids = ['sys_model', 'sys_model@1', 'sys_model@2', ...]`)
* If `model_id`'s are not specified or duplicate, the label is auto-generated as a string indicating the
system model index within `cadCAD.configuration.Experiment().configs`.
(Example of unspecified system models at indexes 1, 3, and 4:
(Example of unspecified system models at indexes 1, 3, and 4:
`cadCAD.configuration.Experiment().model_ids = ['sys_model', '1', 'sys_model@2', '3', '4', ...]`)
* ##### [Upgrade Guide:](https://github.com/cadCAD-org/cadCAD/blob/master/documentation/cadCAD-v0.4.28-Model-Upgrade-Guide.md) specific to feature changes / additions
* #### [Upgrade Guide:](https://github.com/cadCAD-org/cadCAD/blob/master/documentation/cadCAD-v0.4.28-Model-Upgrade-Guide.md) specific to feature changes / additions


### August 25, 2021
#### New Features:
## August 25, 2021
### New Features:
* **ver. ≥ `0.4.27`:**
* ##### [Experiments](documentation#experiments)
* ##### System Model Configurations
* Configurations (`cadCAD.utils.Configuration`'s) as are no longer a part of the `cadCAD` module
* #### [Experiments](documentation#experiments)
* #### System Model Configurations
* Configurations (`cadCAD.utils.Configuration`'s) as are no longer a part of the `cadCAD` module
(as `cadCAD.configs`) and are now accessed via the `configs` member of `cadCAD.configuration.Experiment`.
[Example:](documentation#experiments) `cadCAD.configuration.Experiment().configs`
* ##### Experiments
* `cadCAD.configuration.Experiment` is unique representation of an experiment of one or more configured System
Models. An `Experiment`'s `append_model` method stores multiple system model `Configuration`'s for simulation
* #### Experiments
* `cadCAD.configuration.Experiment` is unique representation of an experiment of one or more configured System
Models. An `Experiment`'s `append_model` method stores multiple system model `Configuration`'s for simulation
execution.
* The `Experiment`'s `append_model` method requires a `model_id` parameter that is auto-created as `'sys_model_#'`.
* **Requirements:**
* **Requirements:**
* Users must use different `model_id`'s when appending multiple System Model Configurations.
* Users can no longer use the `config_list` method of `cadCAD.configuration.Experiment`
* **Backwards Compatibility:** The `append_model` method of `cadCAD.configuration.Experiment` can also be used as
* **Backwards Compatibility:** The `append_model` method of `cadCAD.configuration.Experiment` can also be used as
the `append_configs` method.
* Removed [Nix](https://nixos.org/)
* ##### [Upgrade Guide:](https://github.com/cadCAD-org/cadCAD/blob/master/documentation/cadCAD-v0.4.27-Model-Upgrade-Guide.md) specific to feature changes / additions
* **Fixes:**
* #### [Upgrade Guide:](https://github.com/cadCAD-org/cadCAD/blob/master/documentation/cadCAD-v0.4.27-Model-Upgrade-Guide.md) specific to feature changes / additions
* **Fixes:**
* [#248](https://github.com/cadCAD-org/cadCAD/issues/248)
* The previous release was returning partial results. An A/B test for this has been included and will be for
* The previous release was returning partial results. An A/B test for this has been included and will be for
future releases
* [#242](https://github.com/cadCAD-org/cadCAD/issues/242)
* Parallelized simulations enabled with the re-inclusion of `ProcessPool`.
Expand All @@ -83,26 +92,26 @@
* [#252](https://github.com/cadCAD-org/cadCAD/issues/252)
* Jupyter lab and Jupyter notebook recognises cadCAD module

### September 22, 2020
##### [Multi - System Model Execution](https://github.com/cadCAD-org/cadCAD/blob/master/documentation/Simulation_Execution.md#multiple-simulation-execution)

## September 22, 2020
#### [Multi - System Model Execution](https://github.com/cadCAD-org/cadCAD/blob/master/documentation/Simulation_Execution.md#multiple-simulation-execution)
* **ver. ≥ `0.4.23`:**
* **Hot-Fix:** [#203](https://github.com/cadCAD-org/cadCAD/pull/203) (**No Breaking Changes**)
* Multi - System Model simulation results will no longer return truncated results (exclude the results of the last
* Multi - System Model simulation results will no longer return truncated results (exclude the results of the last
`cadCAD.configuration.Configuration` appended to `cadCAD.configs`).
* Issue: [#195](https://github.com/cadCAD-org/cadCAD/issues/195)
* Parameter Sweep value `M` (Params) requires up to a maximum of 2 distinct lengths


### August 5, 2020
##### [Experiments](documentation#experiments)
* `cadCAD.configuration.Experiment` (Alpha) is in development and needed to be released to support the implementation of
web applications and proprietary feature extensions. It is intended to represent a unique identifier of an experiment of
one or more configured System Models. For this reason, `append_configs` is a method of
`cadCAD.configuration.Experiment`. As of now it does not support multi - system model simulation because configurations
## August 5, 2020
#### [Experiments](documentation#experiments)
* `cadCAD.configuration.Experiment` (Alpha) is in development and needed to be released to support the implementation of
web applications and proprietary feature extensions. It is intended to represent a unique identifier of an experiment of
one or more configured System Models. For this reason, `append_configs` is a method of
`cadCAD.configuration.Experiment`. As of now it does not support multi - system model simulation because configurations
are still appended globally despite `append_config` being a method of Experiment.

###### Examples:
##### Examples:
* **ver. ≥ `0.4.22`:**
```python
from cadCAD.configuration import Experiment
Expand All @@ -116,69 +125,69 @@ are still appended globally despite `append_config` being a method of Experiment
```


### June 22, 2020
## June 22, 2020
* Bug Fix: Multiprocessing error for Windows


### June 19, 2020
### New Features:
##### [Local Execution Mode (Default)](documentation/Simulation_Execution.md#simulation-execution-modes)
* Local Execution Mode (Default): Implicit parallelization of Monte-Carlo / Stochastic simulations (Automatically
## June 19, 2020

## New Features:
#### [Local Execution Mode (Default)](documentation/Simulation_Execution.md#simulation-execution-modes)
* Local Execution Mode (Default): Implicit parallelization of Monte-Carlo / Stochastic simulations (Automatically
selects Multi-Threaded Mode if simulations are configured for more than a single run)
* **Backwards Compatibility:** `cadCAD.engine.ExecutionMode` accepts legacy execution modes from ver. `0.3.1`
###### Examples:

##### Examples:
* **ver. ≥ `0.4.22`:**
```python
from cadCAD.engine import ExecutionMode, ExecutionContext
exec_mode = ExecutionMode()
local_ctx = ExecutionContext(context=exec_mode.local_mode)
```
* **ver. `0.3.1`:**
* **ver. `0.3.1`:**

Multi-Threaded:
```python
from cadCAD.engine import ExecutionMode, ExecutionContext

exec_mode = ExecutionMode()
single_ctx = ExecutionContext(context=exec_mode.multi_proc)
```

Single-Thread:
```python
from cadCAD.engine import ExecutionMode, ExecutionContext

exec_mode = ExecutionMode()
multi_ctx = ExecutionContext(context=exec_mode.single_proc)
```


##### cadCAD Post-Processing Enhancements / Modifications
* [**Single Result Dataset**](documentation/Simulation_Execution.md#4-execute-simulation--produce-system-event-dataset)

#### cadCAD Post-Processing Enhancements / Modifications
* [**Single Result Dataset**](documentation/Simulation_Execution.md#4-execute-simulation--produce-system-event-dataset)
as a 2 dimensional `list`
* Returns a single dataset instead of multiple datasets per Monte Carlo simulation as in `0.3.1`:
* New System Metrics as dataset attributes:
* **Simulation** (Alpha) is a unique identifier being developed to represent Experiments as stated above and
* New System Metrics as dataset attributes:
* **Simulation** (Alpha) is a unique identifier being developed to represent Experiments as stated above and
will be renamed accordingly
* **Subset** is a unique identifier of Monte-Carlo simulations produced by parameter sweeps
* Note: Returning a single dataset was originally specified during the project’s inception instead of multiple per
* Note: Returning a single dataset was originally specified during the project’s inception instead of multiple per
simulation

###### Examples:
##### Examples:
* **ver. ≥ `0.4.22`:**
```python
import pandas as pd
from tabulate import tabulate
from cadCAD.engine import ExecutionMode, ExecutionContext, Executor
import system_model_A, system_model_B
from cadCAD import configs

exec_mode = ExecutionMode()
local_ctx = ExecutionContext(context=exec_mode.local_mode)
simulation = Executor(exec_context=local_ctx, configs=configs)
raw_result, sys_model, _ = simulation.execute()

result = pd.DataFrame(raw_result)
print(tabulate(result, headers='keys', tablefmt='psql'))
```
Expand All @@ -204,12 +213,12 @@ as a 2 dimensional `list`
from cadCAD.engine import ExecutionMode, ExecutionContext, Executor
import system_model_A, system_model_B
from cadCAD import configs

exec_mode = ExecutionMode()

multi_ctx = ExecutionContext(context=exec_mode.multi_proc)
simulation = Executor(exec_context=multi_ctx, configs=configs)

i = 0
config_names = ['sys_model_A', 'sys_model_B']
for raw_result, _ in simulation.execute():
Expand All @@ -235,64 +244,64 @@ as a 2 dimensional `list`
| 7 | ['c', 'd'] | [ 30 300] | 5 | 2018-10-01 15:16:25 | 1 | 3 | 1 |
+----+------------+-----------+----+---------------------+-----+---------+----------+
```
* **Flattened Configuration list:** The `cadCAD.configs` (System Model Configuration) `list` has been **temporarily**
flattened to contain single run `cadCAD.configuration.Configuration` objects to both fault-tolerant simulation and
elastic workloads. This functionality will be restored in a subsequent release by a class that returns

* **Flattened Configuration list:** The `cadCAD.configs` (System Model Configuration) `list` has been **temporarily**
flattened to contain single run `cadCAD.configuration.Configuration` objects to both fault-tolerant simulation and
elastic workloads. This functionality will be restored in a subsequent release by a class that returns
`cadCAD.configs`'s original representation in ver. `0.3.1`.
* The conversion utilities have been provided to restore its original representation of configurations with
* The conversion utilities have been provided to restore its original representation of configurations with
runs >= 1
* [System Configuration Conversions](documentation/System_Configuration.md)
* Configuration as list of Configuration Objects (as in ver. `0.3.1`)
* Configuration as list of Configuration Objects (as in ver. `0.3.1`)
* New: System Configuration as a Pandas DataFrame
* New: System Configuration as list of Dictionaries
###### Examples:

##### Examples:
* Notes:
* `configs` is temporarily returned in a flattened format and reformatted into its intended format
* `Configuration` objects at `0x10790e470` and `0x1143dd630` are reconstituted into objects at `0x10790e7b8`
* `configs` is temporarily returned in a flattened format and reformatted into its intended format
* `Configuration` objects at `0x10790e470` and `0x1143dd630` are reconstituted into objects at `0x10790e7b8`
and `0x116268908` respectively.
* **ver. ≥ `0.4.22`:**
* **ver. ≥ `0.4.22`:**
```python
from pprint import pprint
from documentation.examples import sys_model_A, sys_model_B
from cadCAD.configuration.utils import configs_as_objs, configs_as_dataframe, configs_as_dicts
from cadCAD import configs

flattened_configs = configs
print('Flattened Format: Temporary')

print('Flattened Format: Temporary')
pprint(flattened_configs)
print()

print('Intended Format:')
intended_configs = configs_as_objs(flattened_configs)
pprint(intended_configs)
print()
```

Result:
```bash
Flattened Format: Temporary
[<cadCAD.configuration.Configuration object at 0x10790e470>,
<cadCAD.configuration.Configuration object at 0x10790e7b8>,
<cadCAD.configuration.Configuration object at 0x1143dd630>,
<cadCAD.configuration.Configuration object at 0x116268908>]

Intended Format:
[<cadCAD.configuration.Configuration object at 0x10790e7b8>,
<cadCAD.configuration.Configuration object at 0x116268908>]
```


##### Expandable state and policy update parameter space:
* Enables the development of feature enhancements that involve the use of additional parameters without requiring users
to modify their update parameters spaces when upgrading to newer versions. For this reason state / policy update
#### Expandable state and policy update parameter space:
* Enables the development of feature enhancements that involve the use of additional parameters without requiring users
to modify their update parameters spaces when upgrading to newer versions. For this reason state / policy update
examples in documentation include an additional `**kwargs` parameter.
* [State Updates](documentation/README.md#state-update-functions)
* [Policy Updates](documentation/README.md#state-update-functions)
###### Examples:

##### Examples:
* **ver. ≥ `0.4.22`:**
```python
def state_update(_params, substep, sH, s, _input, **kwargs):
Expand All @@ -316,7 +325,7 @@ examples in documentation include an additional `**kwargs` parameter.
```


### May 29, 2020
* Packaging: Add [Nix](https://nixos.org/) derivation and shell for local development and distribution of cadCAD package
using Nix. Nix is a powerful package manager for Linux and other Unix systems that makes package management reliable and
## May 29, 2020
* Packaging: Add [Nix](https://nixos.org/) derivation and shell for local development and distribution of cadCAD package
using Nix. Nix is a powerful package manager for Linux and other Unix systems that makes package management reliable and
reproducible, allowing you to share your development and build environments across different machines.
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