fixed seq read error

Author: lmdu

.github/workflows/wheel.yml

@@ -8,14 +8,14 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [windows-2019, ubuntu-20.04, macos-13]
+        os: [windows-2022, ubuntu-22.04, macos-15, macos-15-intel]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Set up QEMU
         if: runner.os == 'Linux'
@@ -24,12 +24,11 @@ jobs:
           platforms: all
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.22.0
+        uses: pypa/cibuildwheel@v3.3.1
         env:
-          CIBW_SKIP: pp*
+          CIBW_SKIP: pp* gp*
           CIBW_BUILD_VERBOSITY: 0
-          #CIBW_ARCHS_LINUX: auto aarch64
-          #CIBW_ARCHS_MACOS: x86_64 arm64 universal2
+          CIBW_ARCHS: auto64
           CIBW_TEST_COMMAND: python {project}/setup.py build_ext -i && pytest {project}/tests
           CIBW_TEST_REQUIRES: pyfaidx==0.5.8 pytest
 
@@ -46,12 +45,12 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         name: Install Python
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Build sdist
         run: python setup.py sdist
@@ -69,7 +68,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v5
         with:
           pattern: artifact-*
           merge-multiple: true

.gitignore

@@ -93,3 +93,7 @@ indexed_gzip-1.9.4.zip
 pyfastx.cpython-39-darwin.so
 sqlite-amalgamation-3470200.zip
 zlib-1.3.1.zip
+/indexed_gzip-1.10.3
+indexed_gzip-1.10.3.zip
+pyfastx.cpython-312-x86_64-linux-gnu.so
+src.zip

setup.py

@@ -54,9 +54,9 @@ def prepare_indexed_gzip():
     global include_dirs
     global sources
 
-    igzip_dir = os.path.join(root_dir, "indexed_gzip-1.9.4", "indexed_gzip")
-    igzip_file = os.path.join(root_dir, "indexed_gzip-1.9.4.zip")
-    url = "https://github.com/pauldmccarthy/indexed_gzip/archive/refs/tags/v1.9.4.zip"
+    igzip_dir = os.path.join(root_dir, "indexed_gzip-1.10.3", "indexed_gzip")
+    igzip_file = os.path.join(root_dir, "indexed_gzip-1.10.3.zip")
+    url = "https://github.com/pauldmccarthy/indexed_gzip/archive/refs/tags/v1.10.3.zip"
 
     if not os.path.exists(igzip_dir):
         if not os.path.isfile(igzip_file):
@@ -168,14 +168,13 @@ def build_extensions(self):
             "Natural Language :: English",
             "License :: OSI Approved :: MIT License",
             "Programming Language :: C",
-            "Programming Language :: Python :: 3.6",
-            "Programming Language :: Python :: 3.7",
             "Programming Language :: Python :: 3.8",
             "Programming Language :: Python :: 3.9",
             "Programming Language :: Python :: 3.10",
             "Programming Language :: Python :: 3.11",
             "Programming Language :: Python :: 3.12",
             "Programming Language :: Python :: 3.13",
+            "Programming Language :: Python :: 3.14",
             "Operating System :: Microsoft :: Windows",
             "Operating System :: POSIX :: Linux",
             "Operating System :: Unix",

src/fasta.c

@@ -208,6 +208,11 @@ PyObject * pyfastx_fasta_slice_from_cache(pyfastx_Fasta *self, Py_ssize_t start,
 
 	PyObject *ret;
 
+	if (flank < 0) {
+		PyErr_SetString(PyExc_ValueError, "Flank length must be non-negative");
+		return NULL;
+	}
+
 	slice_start = start - flank - 1;
 	if (slice_start < 0) {
 		slice_len = flank + slice_start;

src/read.c

@@ -54,6 +54,10 @@ void pyfastx_read_continue_reader(pyfastx_Read *self) {
     Py_ssize_t offset;
     Py_ssize_t offset1;
 
+    if (self->raw) {
+        return;
+    }
+
     //read raw string offset
     offset = self->seq_offset - self->desc_len - 1;
     offset1 = offset;
@@ -251,12 +255,14 @@ PyObject* pyfastx_read_quali(pyfastx_Read *self, void* closure) {
     PyObject *quals;
     PyObject *q;
 
-    if (self->middle->iterating) {
-        pyfastx_read_continue_reader(self);
-    } else if (!self->qual) {
-        self->qual = (char *)malloc(self->read_len + 1);
-        pyfastx_read_random_reader(self, self->qual, self->qual_offset, self->read_len);
-        self->qual[self->read_len] = '\0';
+    if (!self->qual) {
+        if (self->middle->iterating) {
+            pyfastx_read_continue_reader(self);
+        } else {
+            self->qual = (char *)malloc(self->read_len + 1);
+            pyfastx_read_random_reader(self, self->qual, self->qual_offset, self->read_len);
+            self->qual[self->read_len] = '\0';
+        }
     }
 
     phred = self->middle->phred ? self->middle->phred : 33;

src/sequence.c

@@ -14,6 +14,10 @@ void pyfastx_sequence_continue_read(pyfastx_Sequence* self) {
 	Py_ssize_t gap;
 	Py_ssize_t rlen;
 
+	if (self->raw) {
+		return;
+	}
+
 	//raw string offset and bytelen
 	header_len = self->desc_len + self->end_len + 1;
 	offset = self->offset - header_len;