biocore · qiyunzhu · May 30, 2025 · May 31, 2025 · May 31, 2025 · May 31, 2025
diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
@@ -10,7 +10,7 @@ on:
 
 env:
   latest_python: "3.13"
-  supported_pythons: '["3.9", "3.10", "3.11", "3.12", "3.13"]'
+  supported_pythons: '["3.10", "3.11", "3.12", "3.13"]'
   miniforge_version: "23.11.0-0"
   miniforge_variant: "Mambaforge"
 

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -6,7 +6,7 @@ on:
       - '*'
 
 env:
-  earliest_python: "3.9"
+  earliest_python: "3.10"
   latest_python: "3.13"
   miniforge_version: "23.11.0-0"
   miniforge_variant: "Mambaforge"
@@ -16,10 +16,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: 3.10
       - name: Build distribution
         run: |
           # set version from '${{ github.ref_name }}'

diff --git a/.gitignore b/.gitignore
@@ -3,6 +3,10 @@
 *.pyc
 biom_format.egg-info/
 
+# Cython converted files
+########################
+*.c
+
 # Cython compiled files
 #######################
 *.so

diff --git a/ChangeLog.md b/ChangeLog.md
@@ -4,6 +4,10 @@ BIOM-Format ChangeLog
 biom-2.1.16-dev
 ---------------
 
+Important:
+
+* The underlying data structure has been migrated from SciPy sparse matrix (spmatrix) to sparse array (sparray). See PR[#993](https://github.com/biocore/biom-format/pull/993). This change does not affect any public-facing API of biom-format. However, be minded that the downstream analysis of data extracted from a BIOM table may be impacted by the API change in sparray vs. spmatrix. See SciPy's documentation: https://docs.scipy.org/doc/scipy/reference/sparse.html for details. This change requires SciPy >= 1.8.0. See its release note: https://docs.scipy.org/doc/scipy/release/1.8.0-notes.html for details.
+
 Performance improvements:
 
 * Decreased execution time of `import biom` by half with lazy imports. See PR[#987](https://github.com/biocore/biom-format/pull/987)

diff --git a/biom/_filter.pyx b/biom/_filter.pyx
@@ -116,7 +116,7 @@ def _filter(arr, ids, metadata, index, ids_to_keep, axis, invert):
         arr = arr.tocsr()
     elif axis == 1:
         arr = arr.tocsc()
-    fmt = arr.getformat()
+    fmt = arr.format
 
     cdef cnp.ndarray[cnp.uint8_t, ndim=1] bools
 

diff --git a/biom/_subsample.pyx b/biom/_subsample.pyx
@@ -21,9 +21,9 @@ cdef _subsample_with_replacement(cnp.ndarray[cnp.float64_t, ndim=1] data,
 
     Parameters
     ----------
-    data : {csr_matrix, csc_matrix}.data
+    data : {csr_array, csc_array}.data
         A 1xM sparse vector data
-    indptr : {csr_matrix, csc_matrix}.indptr
+    indptr : {csr_array, csc_array}.indptr
         A 1xM sparse vector indptr
     n : int
         Number of items to subsample from `arr`
@@ -66,9 +66,9 @@ cdef _subsample_without_replacement(cnp.ndarray[cnp.float64_t, ndim=1] data,
 
     Parameters
     ----------
-    data : {csr_matrix, csc_matrix}.data
+    data : {csr_array, csc_array}.data
         A 1xM sparse vector data
-    indptr : {csr_matrix, csc_matrix}.indptr
+    indptr : {csr_array, csc_array}.indptr
         A 1xM sparse vector indptr
     n : int
         Number of items to subsample from `arr`
@@ -153,7 +153,7 @@ def subsample(arr, n, with_replacement, rng):
 
     Parameters
     ----------
-    arr : {csr_matrix, csc_matrix}
+    arr : {csr_array, csc_array}
         A 1xM sparse vector
     n : int
         Number of items to subsample from `arr`

diff --git a/biom/_transform.pyx b/biom/_transform.pyx
@@ -20,7 +20,7 @@ def _transform(arr, ids, metadata, function, axis):
 
     Parameters
     ----------
-    arr : csr_matrix or csc_matrix
+    arr : csr_array or csc_array
         Matrix whose rows or columns (respectively) are to be
         transformed.
     ids : 1D array_like

diff --git a/biom/cli/installation_informer.py b/biom/cli/installation_informer.py
@@ -8,6 +8,7 @@
 
 
 import sys
+from importlib.metadata import version, PackageNotFoundError
 
 import click
 
@@ -63,25 +64,25 @@ def _get_dependency_version_info():
     not_installed_msg = "Not installed"
 
     try:
-        from click import __version__ as click_lib_version
-    except ImportError:
+        click_lib_version = version("click")
+    except PackageNotFoundError:
         click_lib_version = not_installed_msg
 
     try:
-        from numpy import __version__ as numpy_lib_version
-    except ImportError:
+        numpy_lib_version = version("numpy")
+    except PackageNotFoundError:
         numpy_lib_version = ("ERROR: Not installed - this is required! "
                              "(This will also cause the BIOM library to "
                              "not be importable.)")
 
     try:
-        from scipy import __version__ as scipy_lib_version
-    except ImportError:
+        scipy_lib_version = version("scipy")
+    except PackageNotFoundError:
         scipy_lib_version = not_installed_msg
 
     try:
-        from h5py import __version__ as h5py_lib_version
-    except ImportError:
+        h5py_lib_version = version("h5py")
+    except PackageNotFoundError:
         h5py_lib_version = ("WARNING: Not installed - this is an optional "
                             "dependency. It is strongly recommended for "
                             "large datasets.")
@@ -97,8 +98,8 @@ def _get_package_info():
                         "numpy) - is it installed and in your "
                         "$PYTHONPATH?")
     try:
-        from biom import __version__ as biom_lib_version
-    except ImportError:
+        biom_lib_version = version("biom-format")
+    except PackageNotFoundError:
         biom_lib_version = import_error_msg
 
     return (("biom-format version", biom_lib_version),)