Changes from devel for 0.11.0 release

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.10.9
+current_version = 0.11.0
 commit = True
 
 [bumpversion:file:setup.py]

.github/workflows/conda-publish-manual.yml

@@ -15,7 +15,7 @@ jobs:
             target-platform: linux-64
           - os: ubuntu-24.04-arm
             target-platform: linux-aarch64
-          - os: macos-13
+          - os: macos-15
             target-platform: osx-64
           - os: macos-latest
             target-platform: osx-arm64

.github/workflows/conda-publish.yml

@@ -14,7 +14,7 @@ jobs:
             target-platform: linux-64
           - os: ubuntu-24.04-arm
             target-platform: linux-aarch64
-          - os: macos-13
+          - os: macos-15
             target-platform: osx-64
           - os: macos-latest
             target-platform: osx-arm64

.github/workflows/main.yml

@@ -1,39 +1,52 @@
 name: netZooPy
 
 on:
-  push:
+  push: 
     branches:
       - master
       - devel
-  pull_request:
-    branches:
+  pull_request: 
+    branches: 
       - master
       - devel
 
-jobs:
+jobs: 
   build:
     runs-on: ${{ matrix.os }}
     strategy:
-      matrix:
-        os: [macos-13, ubuntu-latest]
-        python-version: [3.8, 3.9, '3.10']
+      matrix: 
+        os: [macos-15, ubuntu-latest]
+        python-version: [3.9, '3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
+        with: 
+          python-version:  ${{ matrix.python-version }}
       - name: Install dependencies and build package
         run: |
           python -m pip install --upgrade pip
           pip install flake8 pytest pytest-cov codecov
           echo ${{ matrix.os }}
-          if [[ "${{ matrix.os }}" == "macos-latest" ]];then echo "running this";brew install hdf5 c-blosc;export HDF5_DIR=/opt/homebrew/Cellar/hdf5/;export BLOSC_DIR=/opt/homebrew/Cellar/c-blosc/;fi
+          if [[ "${{ matrix.os }}" =~ ^macos- ]]; then 
+            brew install hdf5 c-blosc lzo
+            export HDF5_DIR=$(brew --prefix hdf5)
+            export BLOSC_DIR=$(brew --prefix c-blosc)
+            export LZO_DIR=$(brew --prefix lzo)
+            # Set library and include paths for macOS
+            export LDFLAGS="-L$(brew --prefix hdf5)/lib -L$(brew --prefix c-blosc)/lib -L$(brew --prefix lzo)/lib"
+            export CPPFLAGS="-I$(brew --prefix hdf5)/include -I$(brew --prefix c-blosc)/include -I$(brew --prefix lzo)/include"
+            export PKG_CONFIG_PATH="$(brew --prefix hdf5)/lib/pkgconfig:$(brew --prefix c-blosc)/lib/pkgconfig"
+          fi
+          if [[ "${{ matrix.os }}" =~ ^ubuntu- ]]; then
+            sudo apt-get update
+            sudo apt-get install -y liblzo2-dev libhdf5-dev libblosc-dev
+          fi
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
           pip install -e .
       - name: Lint with flake8
-        run: |
+        run:  |
           # 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
@@ -43,4 +56,4 @@ jobs:
           pytest --cov=netZooPy tests
       - name: Report coverage
         run: |
-          codecov
+          codecov

.github/workflows/test-conda-build.yml

@@ -16,7 +16,7 @@ jobs:
             target-platform: linux-64
           - os: ubuntu-24.04-arm
             target-platform: linux-aarch64
-          - os: macos-13
+          - os: macos-15
             target-platform: osx-64
           - os: macos-latest
             target-platform: osx-arm64

.gitignore

@@ -53,9 +53,13 @@ panda_remove.txt
 pan_test_panda.txt
 tests/lioness/dragon/lioness_dragon_results/
 docs/_build/
-netZooPy/panda/io.py
+#netZooPy/panda/io.py
 debug_bonobo.py
 
 !recipe/
 !recipe/recipe.yaml
-!recipe/test.py
+!recipe/test.py
+
+pixi/*
+.pixi/*
+pixi*

README.md

@@ -108,4 +108,4 @@ Please report any issues to the [issues page](https://github.com/netZoo/netZooPy
 
 Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
 
-Latest version: 0.10.9
+Latest version: 0.11.0

conda/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: netzoopy
-  version: 0.10.9
+  version: 0.11.0
 
 source:
   path: ..
@@ -23,6 +23,7 @@ requirements:
     - click
     - pandas
     - pytables
+    - pytorch
   run:
     - numpy>=1.19.2
     - python {{ python }}
@@ -36,6 +37,7 @@ requirements:
     - click
     - pandas
     - pytables
+    - pytorch
 
 test:
   commands:

docs/conf.py

@@ -29,7 +29,7 @@
 author    = u'netZoo'
 
 # The short X.Y version
-__version__ = "0.10.9"
+__version__ = "0.11.0"
 version     = ".".join(__version__.split(".")[:2])
 # The full version, including alpha/beta/rc tags
 release     = __version__

netZooPy/__init__.py

@@ -7,5 +7,6 @@
 from netZooPy import condor
 from netZooPy import sambar
 from netZooPy import bonobo
+from netZooPy import giraffe 
 
-__version__ = "0.10.9"
+__version__ = "0.11.0"

netZooPy/dragon/dragon.py

@@ -275,7 +275,10 @@ def estimate_kappa_dragon(n, p1, p2, lambdas, seed, simultaneous = False):
             Dlogli11 = lambda x: (1./4*p1*(p1-1)
                             *(sc.digamma(x/2)-sc.digamma((x-1)/2))
                             +term_Dlogli11)
-            kappa11 = optimize.bisect(Dlogli11, 1.001, 1000*n)
+            try:
+                kappa11 = optimize.bisect(Dlogli11, 1.001, 1000*n)
+            except ValueError:
+                raise Exception("[dragon.estimate_kappa_dragon] Unable to optimize kappa11, likely due to high p, low n. \n Consider use of dragon.estimate_p_values_mc instead if p is reasonably small (~1000).")
         else:
             kappa11 = np.nan
 
@@ -284,7 +287,11 @@ def estimate_kappa_dragon(n, p1, p2, lambdas, seed, simultaneous = False):
             Dlogli22 = lambda x: (1./4*p2*(p2-1)
                             *(sc.digamma(x/2)-sc.digamma((x-1)/2))
                             +term_Dlogli22)
-            kappa22 = optimize.bisect(Dlogli22, 1.001, 1000*n)
+            try:
+                kappa22 = optimize.bisect(Dlogli22, 1.001, 1000*n)
+            except ValueError:
+                raise Exception("[dragon.estimate_kappa_dragon] Unable to optimize kappa22, likely due to high p, low n. \n Consider use of dragon.estimate_p_values_mc instead if p is reasonably small (~1000)")
+
         else:
             kappa22 = np.nan
 
@@ -293,7 +300,11 @@ def estimate_kappa_dragon(n, p1, p2, lambdas, seed, simultaneous = False):
             Dlogli12 = lambda x: (1./2*p1*p2
                             *(sc.digamma(x/2)-sc.digamma((x-1)/2))
                             +term_Dlogli12)
-            kappa12 = optimize.bisect(Dlogli12, 1.001, 1000*n)
+            try:
+                kappa12 = optimize.bisect(Dlogli12, 1.001, 1000*n)
+            except ValueError:
+                raise Exception("[dragon.estimate_kappa_dragon] Unable to optimize kappa12, likely due to high p, low n. \n Consider use of dragon.estimate_p_values_mc instead if p is reasonably small (~1000)")
+
         else:
             kappa12 = np.nan
 
@@ -427,8 +438,12 @@ def assign_p_to_r(r_target, r_null, idx1, idx2, verbose=True):
     if np.min(r_null)<0:
         return("[netZooPy.dragon.dragon.assign_p_to_r] Error: null distribution must be absoluted before using this function")
     return np.sum(r_null>np.abs(r_target))/len(r_null)
-
+
+
 def estimate_p_values_mc(r, n, p1, p2, lambdas, seed = 1, verbose = True):
+    if(p1 + p2 > 2000):
+        print("[dragon.estimate_p_values_mc] This function may be prohibitively slow for larger values of p1 + p2. Speed improvements are work in progress. \n Consider thresholding by magnitude instead of p-values.")
+
     lam = lambdas
     r_null = MC_estimate(n, p1, p2,lam, seed) 
 
@@ -496,7 +511,7 @@ def estimate_p_values_mc(r, n, p1, p2, lambdas, seed = 1, verbose = True):
     # adj_pvalues_mat += adj_pvalues_mat.T
 
     return(mc_p)
-
+    
 def calculate_true_R(X1, X2, Sigma):
     x = np.arange(0., 1.01, 0.01)
     n_lams = len(x)

netZooPy/giraffe/__init__.py

@@ -0,0 +1,4 @@
+from __future__ import absolute_import
+
+from .giraffe import Giraffe
+from .utils import *