remove h5py from requirements and tests

Author: hossam26644

python/requirements/CI-complete/requirements.txt

@@ -1,7 +1,6 @@
 biopython==1.85
 coverage==7.7.0
 dendropy==5.0.1
-h5py==3.13.0
 kastore==0.3.3
 lshmm==0.0.8
 msgpack==1.1.0

python/requirements/CI-tests-conda/requirements.txt

@@ -1,4 +1,3 @@
 msprime==1.3.3
 tszip==0.2.5
-h5py==3.13.0
 zarr<3

python/requirements/development.txt

@@ -6,7 +6,6 @@ codecov
 coverage
 dendropy
 flake8
-h5py>=2.6.0
 jsonschema>=3.0.0
 jupyter-book>=0.12.1
 kastore
@@ -22,7 +21,7 @@ numpy
 packaging
 portion
 pre-commit
-pyparsing 
+pyparsing
 pysam
 pytest
 pytest-cov

python/requirements/development.yml

@@ -13,7 +13,6 @@ dependencies:
   - dendropy
   - doxygen
   - flake8
-  - h5py>=2.6.0
   - jsonschema>=3.0.0
   - jupyter-book>=0.12.1
   - kastore

python/tests/test_file_format.py

@@ -28,7 +28,6 @@
 import unittest
 import uuid as _uuid
 
-import h5py
 import kastore
 import msprime
 import numpy as np
@@ -868,12 +867,6 @@ def test_load_empty_kastore(self):
         with pytest.raises(exceptions.LibraryError):
             tskit.load(self.temp_file)
 
-    def test_load_non_tskit_hdf5(self):
-        with h5py.File(self.temp_file, "w") as root:
-            root["x"] = np.zeros(10)
-        with pytest.raises(exceptions.FileFormatError):
-            tskit.load(self.temp_file)
-
     def test_old_version_load_error(self):
         ts = msprime.simulate(10, random_seed=1)
         for bad_version in [(0, 1), (0, 8), (2, 0), (CURRENT_FILE_MAJOR - 1, 0)]: