From 86612265fc0302ad86ebed48787530d0b4b95550 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Mon, 24 Jun 2024 13:47:42 -0700
Subject: [PATCH] fix: support for numpy 2.0 (#220)

* remove upper bound requirement on numpy 2.0

* always return float from GetEntropy even if scipy returns a np.float64

* separate pyp uploading step into separate job in release workflow
---
 .github/workflows/release.yml | 30 ++++++++++++++++++++++++------
 poetry.lock                   |  4 ++--
 pyproject.toml                |  2 +-
 trtools/utils/utils.py        |  2 +-
 4 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 1a14fe7b..88afbf89 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -9,12 +9,10 @@ jobs:
   release:
     name: Release
     runs-on: ubuntu-latest
-    environment: release
-    permissions:
-      # IMPORTANT: this permission is mandatory for trusted publishing
-      id-token: write
+    outputs:
+      release_created: ${{ steps.release.outputs.release_created }}
     steps:
-      - uses: GoogleCloudPlatform/release-please-action@v4.0.2
+      - uses: googleapis/release-please-action@v4
         id: release
         with:
           release-type: python
@@ -47,6 +45,26 @@ jobs:
         run: |
           poetry build --ansi -n
 
-      - name: Publish package on PyPI
+      - uses: actions/upload-artifact@v4
         if: ${{ steps.release.outputs.release_created }}
+        with:
+          name: dist
+          path: dist/
+
+  upload_pypi:
+    needs: release
+    runs-on: ubuntu-latest
+    if: ${{ needs.release.outputs.release_created }}
+    environment: release
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+    steps:
+      - name: Get artifacts
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+          path: dist
+
+      - name: Publish package on PyPI
         uses: pypa/gh-action-pypi-publish@v1.8.14
diff --git a/poetry.lock b/poetry.lock
index 63a6e881..10fe09e9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -1308,4 +1308,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.7.1,<4.0"
-content-hash = "3a18ce16bf6212f78f29a5280d8a96c6454a46a9b09a8faefef32fbc26476259"
+content-hash = "2dbb5553c4b19e25448a8b48a6af0c082d45ebcac72164b45540b3e00360015d"
diff --git a/pyproject.toml b/pyproject.toml
index 6f9071de..3177511e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,7 +35,7 @@ python = ">=3.7.1,<4.0"
 importlib-metadata = {version = ">=3.0.0", python = "<3.8"}
 cyvcf2 = ">=0.30.4"
 matplotlib = ">=3.1.2"
-numpy = ">=1.17.3,<2.0"
+numpy = ">=1.17.3"
 pandas = ">=1.2.0"
 pysam = ">=0.15.4"
 scikit-learn = ">=0.23.1"
diff --git a/trtools/utils/utils.py b/trtools/utils/utils.py
index c1d55955..b76eb547 100644
--- a/trtools/utils/utils.py
+++ b/trtools/utils/utils.py
@@ -196,7 +196,7 @@ def GetEntropy(allele_freqs: Dict[Any, float]) -> float:
     """
     if not ValidateAlleleFreqs(allele_freqs):
         return np.nan
-    return scipy.stats.entropy(list(x for x in allele_freqs.values()), base=2)
+    return float(scipy.stats.entropy(list(x for x in allele_freqs.values()), base=2))
 
 
 def GetMean(allele_freqs):