timeawarepc 2.0.0__tar.gz → 2.0.1__tar.gz

{timeawarepc-2.0.0 → timeawarepc-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: timeawarepc
-Version: 2.0.0
+Version: 2.0.1
 Summary: Time-Aware PC Python Package
 Home-page: https://github.com/biswasr/TimeAwarePC
 Author: Rahul Biswas
@@ -15,7 +15,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: pandas
-Requires-Dist: rpy2==3.5.11
+Requires-Dist: rpy2>=3.5.11
 Requires-Dist: networkx
 Requires-Dist: scipy
 Dynamic: author
@@ -39,11 +39,25 @@ Dynamic: summary
 
 ## Installation
 
-## Requirements
-- Python >=3.7, <3.11
-- Python packages automatically checked and installed as part of the setup. To use Granger Causality, additional dependency of ```nitime``` which can be installed by ```pip install nitime```.
-- R == 4.4.2
-- R package ```kpcalg``` and its dependencies. They can be installed in R or RStudio as follows:
+### Recommended: conda environment (handles R + kpcalg automatically)
+
+```
+$ git clone https://github.com/shlizee/TimeAwarePC.git
+$ cd TimeAwarePC
+$ conda env create -f environment.yml
+$ conda activate timeawarepc
+$ Rscript install_r_deps.R   # installs kpcalg from CRAN archive
+```
+
+This installs Python, R, rpy2, all required R packages (graph, RBGL, pcalg), and TimeAwarePC v2.0.0 in a single isolated environment.
+
+### Manual install (alternative)
+
+If you prefer to install without conda:
+
+- Python >=3.9, <3.11
+- R >= 4.0
+- R package ```kpcalg``` and its dependencies, installed via R or RStudio:
 ```
 > install.packages("BiocManager")
 > BiocManager::install("graph")
@@ -51,17 +65,13 @@ Dynamic: summary
 > install.packages("pcalg")
 > install.packages("https://cran.r-project.org/src/contrib/Archive/kpcalg/kpcalg_1.0.1.tar.gz")
 ```
-<!-- - In addition, if you like to use Granger Causality functions in this package, please separately install nitime as follows:
-```
-pip install nitime
-``` -->
-
-After meeting these requirements, you can get the latest version of TimeAwarePC as follows.
-
+- Then:
 ```
 $ pip install timeawarepc
 ```
 
+To use Granger Causality, also install `nitime` (`pip install nitime`).
+
 ## Documentation
 
 [Documentation is available at readthedocs.org](https://timeawarepc.readthedocs.io/en/latest/)
@@ -70,11 +80,11 @@ $ pip install timeawarepc
 
 See the [Quick Start Guide](https://timeawarepc.readthedocs.io/en/latest/gettingstarted.html) for a quick tutorial of the main functionalities of this library and check if it is installed properly.
 
-## What's new in v2.0.0 (BREAKING)
+## What's new in v2.0.0
 
 - `cfc_tpc` now defaults to **no bootstrap subsampling**: a single PC run is performed on the full time-delayed data.
-  - To enable the legacy bootstrap behavior (50-row windows, 25 iterations), pass `subsampsize=50, niter=25` explicitly.
-  - Both `subsampsize` and `niter` must be specified together (or both left as the default `None`).
+  - To use bootstrap stability scoring, pass `subsampsize` and `niter` together (e.g., `subsampsize=50, niter=25`).
+  - Both arguments must be specified together (or both left as the default `None`).
 - `partial_corr` now fits an intercept and is shift-invariant. Previously the regression was forced through the origin, biasing residuals when the data was not mean-centered.
 - See [CHANGELOG.md](CHANGELOG.md) for the full list of changes and migration notes.
 <!-- 

{timeawarepc-2.0.0 → timeawarepc-2.0.1}/README.md

@@ -7,11 +7,25 @@
 
 ## Installation
 
-## Requirements
-- Python >=3.7, <3.11
-- Python packages automatically checked and installed as part of the setup. To use Granger Causality, additional dependency of ```nitime``` which can be installed by ```pip install nitime```.
-- R == 4.4.2
-- R package ```kpcalg``` and its dependencies. They can be installed in R or RStudio as follows:
+### Recommended: conda environment (handles R + kpcalg automatically)
+
+```
+$ git clone https://github.com/shlizee/TimeAwarePC.git
+$ cd TimeAwarePC
+$ conda env create -f environment.yml
+$ conda activate timeawarepc
+$ Rscript install_r_deps.R   # installs kpcalg from CRAN archive
+```
+
+This installs Python, R, rpy2, all required R packages (graph, RBGL, pcalg), and TimeAwarePC v2.0.0 in a single isolated environment.
+
+### Manual install (alternative)
+
+If you prefer to install without conda:
+
+- Python >=3.9, <3.11
+- R >= 4.0
+- R package ```kpcalg``` and its dependencies, installed via R or RStudio:
 ```
 > install.packages("BiocManager")
 > BiocManager::install("graph")
@@ -19,17 +33,13 @@
 > install.packages("pcalg")
 > install.packages("https://cran.r-project.org/src/contrib/Archive/kpcalg/kpcalg_1.0.1.tar.gz")
 ```
-<!-- - In addition, if you like to use Granger Causality functions in this package, please separately install nitime as follows:
-```
-pip install nitime
-``` -->
-
-After meeting these requirements, you can get the latest version of TimeAwarePC as follows.
-
+- Then:
 ```
 $ pip install timeawarepc
 ```
 
+To use Granger Causality, also install `nitime` (`pip install nitime`).
+
 ## Documentation
 
 [Documentation is available at readthedocs.org](https://timeawarepc.readthedocs.io/en/latest/)
@@ -38,11 +48,11 @@ $ pip install timeawarepc
 
 See the [Quick Start Guide](https://timeawarepc.readthedocs.io/en/latest/gettingstarted.html) for a quick tutorial of the main functionalities of this library and check if it is installed properly.
 
-## What's new in v2.0.0 (BREAKING)
+## What's new in v2.0.0
 
 - `cfc_tpc` now defaults to **no bootstrap subsampling**: a single PC run is performed on the full time-delayed data.
-  - To enable the legacy bootstrap behavior (50-row windows, 25 iterations), pass `subsampsize=50, niter=25` explicitly.
-  - Both `subsampsize` and `niter` must be specified together (or both left as the default `None`).
+  - To use bootstrap stability scoring, pass `subsampsize` and `niter` together (e.g., `subsampsize=50, niter=25`).
+  - Both arguments must be specified together (or both left as the default `None`).
 - `partial_corr` now fits an intercept and is shift-invariant. Previously the regression was forced through the origin, biasing residuals when the data was not mean-centered.
 - See [CHANGELOG.md](CHANGELOG.md) for the full list of changes and migration notes.
 <!-- 

{timeawarepc-2.0.0 → timeawarepc-2.0.1}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = timeawarepc
-version = 2.0.0
+version = 2.0.1
 author = Rahul Biswas
 author_email = rahul.biswas@ucsf.edu
 description = Time-Aware PC Python Package
@@ -24,7 +24,7 @@ python_requires = >=3.7, <3.11
 install_requires = 
 	numpy
 	pandas
-	rpy2==3.5.11
+	rpy2>=3.5.11
 	networkx
 	scipy
 

{timeawarepc-2.0.0 → timeawarepc-2.0.1}/setup.py

@@ -3,7 +3,7 @@ import setuptools
 with open('README.md','r') as fh:
     README = fh.read()
 
-VERSION = "2.0.0"
+VERSION = "2.0.1"
 
 setuptools.setup(
     name = 'timeawarepc',
@@ -19,7 +19,7 @@ setuptools.setup(
     install_requires=[
         'numpy',
         'pandas',
-        'rpy2==3.5.11',
+        'rpy2>=3.5.11',
         'networkx',
         'scipy'
     ],

{timeawarepc-2.0.0 → timeawarepc-2.0.1}/timeawarepc/__init__.py

@@ -2,5 +2,5 @@
 Time-Aware PC Algorithm for estimating Causal Functional Connectivity from Time Series
 """
 
-__version__ = "0.0.1"
+__version__ = "2.0.1"
 __all__ = ["tpc_helpers","tpc","find_cfc","pcalg","pcalg_helpers","simulate_data"]

{timeawarepc-2.0.0 → timeawarepc-2.0.1}/timeawarepc.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: timeawarepc
-Version: 2.0.0
+Version: 2.0.1
 Summary: Time-Aware PC Python Package
 Home-page: https://github.com/biswasr/TimeAwarePC
 Author: Rahul Biswas
@@ -15,7 +15,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: pandas
-Requires-Dist: rpy2==3.5.11
+Requires-Dist: rpy2>=3.5.11
 Requires-Dist: networkx
 Requires-Dist: scipy
 Dynamic: author
@@ -39,11 +39,25 @@ Dynamic: summary
 
 ## Installation
 
-## Requirements
-- Python >=3.7, <3.11
-- Python packages automatically checked and installed as part of the setup. To use Granger Causality, additional dependency of ```nitime``` which can be installed by ```pip install nitime```.
-- R == 4.4.2
-- R package ```kpcalg``` and its dependencies. They can be installed in R or RStudio as follows:
+### Recommended: conda environment (handles R + kpcalg automatically)
+
+```
+$ git clone https://github.com/shlizee/TimeAwarePC.git
+$ cd TimeAwarePC
+$ conda env create -f environment.yml
+$ conda activate timeawarepc
+$ Rscript install_r_deps.R   # installs kpcalg from CRAN archive
+```
+
+This installs Python, R, rpy2, all required R packages (graph, RBGL, pcalg), and TimeAwarePC v2.0.0 in a single isolated environment.
+
+### Manual install (alternative)
+
+If you prefer to install without conda:
+
+- Python >=3.9, <3.11
+- R >= 4.0
+- R package ```kpcalg``` and its dependencies, installed via R or RStudio:
 ```
 > install.packages("BiocManager")
 > BiocManager::install("graph")
@@ -51,17 +65,13 @@ Dynamic: summary
 > install.packages("pcalg")
 > install.packages("https://cran.r-project.org/src/contrib/Archive/kpcalg/kpcalg_1.0.1.tar.gz")
 ```
-<!-- - In addition, if you like to use Granger Causality functions in this package, please separately install nitime as follows:
-```
-pip install nitime
-``` -->
-
-After meeting these requirements, you can get the latest version of TimeAwarePC as follows.
-
+- Then:
 ```
 $ pip install timeawarepc
 ```
 
+To use Granger Causality, also install `nitime` (`pip install nitime`).
+
 ## Documentation
 
 [Documentation is available at readthedocs.org](https://timeawarepc.readthedocs.io/en/latest/)
@@ -70,11 +80,11 @@ $ pip install timeawarepc
 
 See the [Quick Start Guide](https://timeawarepc.readthedocs.io/en/latest/gettingstarted.html) for a quick tutorial of the main functionalities of this library and check if it is installed properly.
 
-## What's new in v2.0.0 (BREAKING)
+## What's new in v2.0.0
 
 - `cfc_tpc` now defaults to **no bootstrap subsampling**: a single PC run is performed on the full time-delayed data.
-  - To enable the legacy bootstrap behavior (50-row windows, 25 iterations), pass `subsampsize=50, niter=25` explicitly.
-  - Both `subsampsize` and `niter` must be specified together (or both left as the default `None`).
+  - To use bootstrap stability scoring, pass `subsampsize` and `niter` together (e.g., `subsampsize=50, niter=25`).
+  - Both arguments must be specified together (or both left as the default `None`).
 - `partial_corr` now fits an intercept and is shift-invariant. Previously the regression was forced through the origin, biasing residuals when the data was not mean-centered.
 - See [CHANGELOG.md](CHANGELOG.md) for the full list of changes and migration notes.
 <!-- 

{timeawarepc-2.0.0 → timeawarepc-2.0.1}/timeawarepc.egg-info/requires.txt

@@ -1,5 +1,5 @@
 numpy
 pandas
-rpy2==3.5.11
+rpy2>=3.5.11
 networkx
 scipy