Nudge of release to minor patched version 2.0.3 (#118)

* nudge of doc to 2.0.2 (#115)

Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu>

* minor edit to math in hh-lesson doc

* Fix workflow, numpy install, and pytest bug in github action workflows (#117)

* Update pyproject.toml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* minor nudge/cleanup to minor patched version 2.0.1

* minor nudge/cleanup to minor patched version 2.0.3

---------

Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu>
Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com>

Author: 3 people

.github/workflows/python-package-conda.yml

@@ -10,25 +10,19 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
+    
+    - name: Install Miniconda
+      uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: '3.10'
-    - name: Add conda to system path
+        auto-update-conda: true
+        python-version: 3.11
+        environment-name: test
+    
+    - name: Install dependencies
       run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install current library and dependencies
-      run: |
-        pip install -e .
-    # - name: Lint with flake8
-    #   run: |
-    #     conda install flake8
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
+        conda install -n test numpy=1.26 pytest pip
+        conda run -n test pip install -e .
+
+    - name: Run tests
       run: |
-        conda install pytest
-        pytest
+        conda run -n test pytest

README.md

@@ -32,7 +32,7 @@ ngc-learn requires:
 1) Python (>=3.10)
 2) NumPy (>=1.22.0)
 3) SciPy (>=1.7.0)
-4) ngcsimlib (>=1.0.0), (visit official page <a href="https://github.com/NACLab/ngc-sim-lib">here</a>)
+4) ngcsimlib (>=1.0.1), (visit official page <a href="https://github.com/NACLab/ngc-sim-lib">here</a>)
 5) JAX (>=0.4.28) (to enable GPU use, make sure to install one of the CUDA variants)
 <!--
 5) scikit-learn (>=1.3.1) if using `ngclearn.utils.density`
@@ -42,7 +42,7 @@ ngc-learn requires:
 -->
 
 ---
-ngc-learn 2.0.0 and later require Python 3.10 or newer as well as ngcsimlib >=1.0.0.
+ngc-learn 2.0.3 and later require Python 3.10 or newer as well as ngcsimlib >=1.0.1.
 ngc-learn's plotting capabilities (routines within `ngclearn.utils.viz`) require
 Matplotlib (>=3.8.0) and imageio (>=2.31.5) and both plotting and density estimation
 tools (routines within ``ngclearn.utils.density``) will require Scikit-learn (>=0.24.2).
@@ -75,7 +75,7 @@ Python 3.11.4 (main, MONTH  DAY YEAR, TIME) [GCC XX.X.X] on linux
 Type "help", "copyright", "credits" or "license" for more information.
 >>> import ngclearn
 >>> ngclearn.__version__
-'2.0.0'
+'2.0.3'
 ```
 
 <i>Note:</i> For access to the previous Tensorflow-2 version of ngc-learn (of
@@ -122,7 +122,7 @@ $ python install -e .
 </pre>
 
 **Version:**<br>
-2.0.2 <!--1.2.3-Beta--> <!-- -Alpha -->
+2.0.3 <!--1.2.3-Beta--> <!-- -Alpha -->
 
 Author:
 Alexander G. Ororbia II<br>

docs/installation.md

@@ -9,7 +9,7 @@ requires that you ensure that you have installed the following base dependencies
 your system. Note that this library was developed and tested on Ubuntu 22.04 (and earlier versions on 18.04/20.04).
 Specifically, ngc-learn requires:
 * Python (>=3.10)
-* ngcsimlib (>=1.0.0), (<a href="https://github.com/NACLab/ngc-sim-lib">official page</a>)
+* ngcsimlib (>=1.0.1), (<a href="https://github.com/NACLab/ngc-sim-lib">official page</a>)
 * NumPy (>=1.22.0)
 * SciPy (>=1.7.0)
 * JAX (>= 0.4.28; and jaxlib>=0.4.28) <!--(tested for cuda 11.8)-->
@@ -78,7 +78,7 @@ Python 3.11.4 (main, MONTH  DAY YEAR, TIME) [GCC XX.X.X] on linux
 Type "help", "copyright", "credits" or "license" for more information.
 >>> import ngclearn
 >>> ngclearn.__version__
-'2.0.2'
+'2.0.3'
 ```
 
 <i>Note</i>: If you do not have a JSON configuration file in place (see tutorials

docs/requirements.txt

@@ -8,4 +8,4 @@ matplotlib>=3.8.0
 jax>=0.4.28
 jaxlib>=0.4.28
 imageio>=2.31.5
-ngcsimlib>=1.0.0
+ngcsimlib>=1.0.1

docs/tutorials/neurocog/hodgkin_huxley_cell.md

@@ -82,7 +82,7 @@ neurons and muscle cells. It is a continuous-time dynamical system.
 Formally, the core dynamics of the H-H cell can be written out as follows:
 
 $$
-\tau_v \frac{\partial \mathbf{v}_t}{\partial t} &= \mathbf{j}_t - g_Na * \mathbf{m}^3_t * \mathbf{h}_t * (\mathbf{v}_t - v_Na) - g_K * \mathbf{n}^4_t * (\mathbf{v}_t - v_K) - g_L * (\mathbf{v}_t - v_L) \\
+\tau_v \frac{\partial \mathbf{v}_t}{\partial t} &= \mathbf{j}_t - g_{Na} * \mathbf{m}^3_t * \mathbf{h}_t * (\mathbf{v}_t - v_{Na}) - g_K * \mathbf{n}^4_t * (\mathbf{v}_t - v_K) - g_L * (\mathbf{v}_t - v_L) \\
 \frac{\partial \mathbf{n}_t}{\partial t} &= \alpha_n(\mathbf{v}_t) * (1 - \mathbf{n}_t) - \beta_n(\mathbf{v}_t) * \mathbf{n}_t \\
 \frac{\partial \mathbf{m}_t}{\partial t} &= \alpha_m(\mathbf{v}_t) * (1 - \mathbf{m}_t) - \beta_m(\mathbf{v}_t) * \mathbf{m}_t \\
 \frac{\partial \mathbf{h}_t}{\partial t} &= \alpha_h(\mathbf{v}_t) * (1 - \mathbf{h}_t) - \beta_h(\mathbf{v}_t) * \mathbf{h}_t

history.txt

@@ -80,3 +80,8 @@ History
   * integration of reinforce-synapse, block/partitioned synapse component ("patched-synapse")
   * basic unit-tests (pytest framework) integrated to support dev
   * includes support for Intel's lava-nc emulator (several spiking/stdp components that play with ngc-lava)
+
+2.0.3
+— — — — — — — — -
+  * Minor patch to point / depend on minor-patched ngcsimlib 1.0.1 (nudge to minor patched release)
+  * Added wrapper `inverse_sigmoid` for original `inverse_logistic` routine in model_utils (for convenience)

ngclearn/utils/model_utils.py

@@ -508,10 +508,13 @@ def d_sigmoid(x):
     sigm_x = nn.sigmoid(x) ## pre-compute once
     return sigm_x * (1. - sigm_x)
 
+def inverse_sigmoid(x, clip_bound=0.03): ## wrapper call for naming convention ease
+    return inverse_logistic(x, clip_bound=clip_bound)
+
 @jit
-def inverse_logistic(x, clip_bound=0.03): # 0.03
+def inverse_logistic(x, clip_bound=0.03):
     """
-    The inverse logistic link - logit function.
+    The inverse logistic link - the logit function.
 
     Args:
         x: data to transform via inverse logistic function

pyproject.toml

@@ -1,10 +1,14 @@
 [build-system]
-requires = ["setuptools>=61.0"]
-build-backend = "setuptools.build_meta"
+requires = [
+  "setuptools>=61.0",    # default
+  "wheel",               # also often needed
+  "numpy>=1.19.5"        # add numpy here for build-time use
+]
+build-backend = "setuptools.build_meta" # using setuptool building engine
 
 [project]
 name = "ngclearn"
-version = "2.0.2"
+version = "2.0.3"
 description = "Simulation software for building and analyzing arbitrary predictive coding, spiking network, and biomimetic neural systems."
 authors = [
   {name = "Alexander Ororbia", email = "ago@cs.rit.edu"},

requirements.txt

@@ -5,6 +5,6 @@ matplotlib>=3.8.0
 patchify
 jax>=0.4.28
 jaxlib>=0.4.28
-ngcsimlib>=1.0.0
+ngcsimlib>=1.0.1
 imageio>=2.31.5
 pandas>=2.2.3