Updates (AliciaCurth#24)

* bump version * Bump version: 0.1.6 * Workflows update: Scheduled runs, updated python versions (#2) * update Py versions * py3.10 fix * update deps * drop 3.10 * updare reqs * debug jaxlib * debug jaxlib * windows debug * debug windows * debug windows * optional JAX, Torch * debug windows * debug windows * bump version * Update .pre-commit-config.yaml * Update .pre-commit-config.yaml * update workflows (#3) * update workflows * debug release * cleanup * Bugfixing (#4) * fix PyTorch API * GPU fixes enable more tests * bugfixing * train/eval review * update JAX (#5)
vanderschaarlab · Sep 3, 2022 · 21782d9 · 21782d9
1 parent bb4da46
commit 21782d9
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diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,73 @@
+name: Package release
+
+on:
+  release:
+    types: [created]
+
+
+jobs:
+  deploy_osx:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        os: [macos-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: true
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: ${GITHUB_WORKSPACE}/.github/workflows/scripts/release_osx.sh
+
+  deploy_linux:
+    strategy:
+      matrix:
+        python-version:
+          - cp37-cp37m
+          - cp38-cp38
+          - cp39-cp39
+          - cp10-cp10
+
+    runs-on: ubuntu-latest
+    container: quay.io/pypa/manylinux2014_x86_64
+    steps:
+      - uses: actions/checkout@v1
+        with:
+          submodules: true
+      - name: Set target Python version PATH
+        run: |
+            echo "/opt/python/${{ matrix.python-version }}/bin" >> $GITHUB_PATH
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: ${GITHUB_WORKSPACE}/.github/workflows/scripts/release_linux.sh
+
+  deploy_windows:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: true
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          ../../.github/workflows/scripts/release_windows.bat
diff --git a/.github/workflows/scripts/release_linux.sh b/.github/workflows/scripts/release_linux.sh
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+set -e
+
+yum makecache -y
+yum install centos-release-scl -y
+yum-config-manager --enable rhel-server-rhscl-7-rpms
+yum install llvm-toolset-7.0 python3 python3-devel -y
+
+# Python
+python3 -m pip install --upgrade pip
+python3 -m pip install setuptools wheel twine auditwheel
+
+# Publish
+python3 -m pip wheel . -w dist/ --no-deps
+twine upload --verbose --skip-existing dist/*
diff --git a/.github/workflows/scripts/release_osx.sh b/.github/workflows/scripts/release_osx.sh
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+export MACOSX_DEPLOYMENT_TARGET=10.14
+
+python -m pip install --upgrade pip
+pip install setuptools wheel twine auditwheel
+
+python3 setup.py build bdist_wheel --plat-name macosx_10_14_x86_64 --dist-dir wheel
+twine upload --skip-existing wheel/*
diff --git a/.github/workflows/scripts/release_windows.bat b/.github/workflows/scripts/release_windows.bat
@@ -0,0 +1,7 @@
+echo on
+
+python -m pip install --upgrade pip
+pip install setuptools wheel twine auditwheel
+
+pip wheel . -w wheel/ --no-deps
+twine upload --skip-existing wheel/*
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -37,7 +37,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9']
+        python-version: ['3.7', '3.8', '3.9', "3.10"]
         os: [macos-latest, ubuntu-latest, windows-latest]
     steps:
       - uses: actions/checkout@v2

diff --git a/catenets/models/jax/base.py b/catenets/models/jax/base.py
@@ -8,8 +8,8 @@
 import jax.numpy as jnp
 import numpy as onp
 from jax import grad, jit, random
-from jax.experimental import optimizers, stax
-from jax.experimental.stax import Dense, Elu, Relu, Sigmoid
+from jax.example_libraries import optimizers, stax
+from jax.example_libraries.stax import Dense, Elu, Relu, Sigmoid
 from sklearn.base import BaseEstimator, RegressorMixin
 from sklearn.model_selection import ParameterGrid
 

diff --git a/catenets/models/jax/disentangled_nets.py b/catenets/models/jax/disentangled_nets.py
@@ -8,7 +8,7 @@
 import jax.numpy as jnp
 import numpy as onp
 from jax import grad, jit, random
-from jax.experimental import optimizers
+from jax.example_libraries import optimizers
 
 import catenets.logger as log
 from catenets.models.constants import (

diff --git a/catenets/models/jax/flextenet.py b/catenets/models/jax/flextenet.py
@@ -8,8 +8,15 @@
 import jax.numpy as jnp
 import numpy as onp
 from jax import grad, jit, random
-from jax.experimental import optimizers
-from jax.experimental.stax import Dense, Sigmoid, elu, glorot_normal, normal, serial
+from jax.example_libraries import optimizers
+from jax.example_libraries.stax import (
+    Dense,
+    Sigmoid,
+    elu,
+    glorot_normal,
+    normal,
+    serial,
+)
 
 import catenets.logger as log
 from catenets.models.constants import (

diff --git a/catenets/models/jax/offsetnet.py b/catenets/models/jax/offsetnet.py
@@ -10,8 +10,8 @@
 import jax.numpy as jnp
 import numpy as onp
 from jax import grad, jit, random
-from jax.experimental import optimizers
-from jax.experimental.stax import sigmoid
+from jax.example_libraries import optimizers
+from jax.example_libraries.stax import sigmoid
 
 import catenets.logger as log
 from catenets.models.constants import (

diff --git a/catenets/models/jax/representation_nets.py b/catenets/models/jax/representation_nets.py
@@ -8,7 +8,7 @@
 import jax.numpy as jnp
 import numpy as onp
 from jax import grad, jit, random
-from jax.experimental import optimizers
+from jax.example_libraries import optimizers
 
 import catenets.logger as log
 from catenets.models.constants import (

diff --git a/catenets/models/jax/rnet.py b/catenets/models/jax/rnet.py
@@ -8,7 +8,7 @@
 import numpy as onp
 import pandas as pd
 from jax import grad, jit, random
-from jax.experimental import optimizers
+from jax.example_libraries import optimizers
 from sklearn.model_selection import StratifiedKFold
 
 import catenets.logger as log
@@ -135,7 +135,7 @@ def __init__(
         n_iter_print: int = DEFAULT_N_ITER_PRINT,
         seed: int = DEFAULT_SEED,
         nonlin: str = DEFAULT_NONLIN,
-        binary_y: bool = False
+        binary_y: bool = False,
     ) -> None:
         # settings
         self.binary_y = binary_y
@@ -243,7 +243,7 @@ def train_r_net(
     seed: int = DEFAULT_SEED,
     return_val_loss: bool = False,
     nonlin: str = DEFAULT_NONLIN,
-    binary_y: bool = False
+    binary_y: bool = False,
 ) -> Any:
     # get shape of data
     n, d = X.shape
@@ -288,7 +288,7 @@ def train_r_net(
             n_iter_print=n_iter_print,
             seed=seed,
             nonlin=nonlin,
-            binary_y=binary_y
+            binary_y=binary_y,
         )
         if data_split:
             # keep only prediction data
@@ -333,7 +333,7 @@ def train_r_net(
                 n_iter_print=n_iter_print,
                 seed=seed,
                 nonlin=nonlin,
-                binary_y=binary_y
+                binary_y=binary_y,
             )
 
     log.debug("Training second stage.")
@@ -415,7 +415,7 @@ def _train_and_predict_r_stage1(
     n_iter_print: int = DEFAULT_N_ITER_PRINT,
     seed: int = DEFAULT_SEED,
     nonlin: str = DEFAULT_NONLIN,
-    binary_y: bool = False
+    binary_y: bool = False,
 ) -> Any:
     if len(w.shape) > 1:
         w = w.reshape((len(w),))
@@ -443,7 +443,7 @@ def _train_and_predict_r_stage1(
         n_iter_print=n_iter_print,
         seed=seed,
         nonlin=nonlin,
-        binary_y=binary_y
+        binary_y=binary_y,
     )
     mu_hat = predict_fun_out(params_out, X_pred)
 

diff --git a/catenets/models/jax/snet.py b/catenets/models/jax/snet.py
@@ -7,7 +7,7 @@
 import jax.numpy as jnp
 import numpy as onp
 from jax import grad, jit, random
-from jax.experimental import optimizers
+from jax.example_libraries import optimizers
 
 import catenets.logger as log
 from catenets.models.constants import (

diff --git a/catenets/models/jax/tnet.py b/catenets/models/jax/tnet.py
@@ -7,7 +7,7 @@
 import jax.numpy as jnp
 import numpy as onp
 from jax import grad, jit, random
-from jax.experimental import optimizers
+from jax.example_libraries import optimizers
 
 import catenets.logger as log
 from catenets.models.constants import (