Merge pull request #112 from deeptools/fix111

.environmentLinux.yaml

@@ -0,0 +1,13 @@
+name: foo
+channels:
+  - conda-forge
+  - bioconda
+  - default
+dependencies:
+  - gcc_linux-64
+  - curl
+  - zlib
+  - python 3.8
+  - pip
+  - numpy
+  - nose

.github/workflows/build.yml

@@ -0,0 +1,19 @@
+on: pull_request
+jobs:
+  testLinux:
+    name: TestLinux
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: foo
+          environment-file: .environmentLinux.yaml
+          python-version: 3.8
+          auto-activate-base: false
+      - run: |
+          pip install .
+          nosetests -sv

.github/workflows/pypi.yml

@@ -0,0 +1,37 @@
+name: pypi
+on: [push]
+jobs:
+  pypi:
+    name: upload to pypi
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: Setup conda
+      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+      run: |
+        curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh
+        bash miniconda.sh -b -p $HOME/miniconda
+        export PATH="$HOME/miniconda/bin:$PATH"
+        hash -r
+        conda config --set always_yes yes --set changeps1 no
+    - name: create env
+      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        conda create -n foo -q --yes -c conda-forge -c bioconda python=3.7 twine numpy libcurl curl zlib
+    - name: sdist
+      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        source activate foo
+        rm -f dist/*
+        python setup.py sdist
+    - name: upload
+      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+      env:
+        TWINE_USERNAME: "__token__"
+        TWINE_PASSWORD: ${{ secrets.pypi_password }}
+      run: |
+        export PATH=$HOME/miniconda/bin:$PATH
+        source activate foo
+        twine upload dist/*

libBigWig/bigWig.h

@@ -1,3 +1,6 @@
+#ifndef LIBBIGWIG_H
+#define LIBBIGWIG_H
+
 #include "bigWigIO.h"
 #include "bwValues.h"
 #include <inttypes.h>
@@ -53,15 +56,18 @@ extern "C" {
 /*!
  * The library version number
  */
-#define LIBBIGWIG_VERSION 0.4.4
+#define LIBBIGWIG_VERSION 0.4.6
 
 /*!
  * If 1, then this library was compiled with remote file support.
  */
 #ifdef NOCURL
 #define LIBBIGWIG_CURL 0
+#ifndef CURLTYPE_DEFINED
+#define CURLTYPE_DEFINED
 typedef int CURLcode;
 typedef void CURL;
+#endif
 #else
 #define LIBBIGWIG_CURL 1
 #endif
@@ -596,3 +602,5 @@ int bwAppendIntervalSpanSteps(bigWigFile_t *fp, float *values, uint32_t n);
 #ifdef __cplusplus
 }
 #endif
+
+#endif // LIBBIGWIG_H

libBigWig/bigWigIO.h

@@ -1,9 +1,15 @@
+#ifndef LIBBIGWIG_IO_H
+#define LIBBIGWIG_IO_H
+
 #ifndef NOCURL
 #include <curl/curl.h>
 #else
 #include <stdio.h>
+#ifndef CURLTYPE_DEFINED
+#define CURLTYPE_DEFINED
 typedef int CURLcode;
 typedef void CURL;
+#endif
 #define CURLE_OK 0
 #define CURLE_FAILED_INIT 1
 #endif
@@ -100,3 +106,5 @@ URL_t *urlOpen(char *fname, CURLcode (*callBack)(CURL*), const char* mode);
  *  @warning URL will no longer point to a valid location in memory!
  */
 void urlClose(URL_t *URL);
+
+#endif // LIBBIGWIG_IO_H

libBigWig/bwRead.c

@@ -371,7 +371,7 @@ bigWigFile_t *bwOpen(char *fname, CURLcode (*callBack) (CURL*), const char *mode
         }
 
         //Read in the index
-        if(bwg->hdr->nBasesCovered) {
+        if(bwg->hdr->indexOffset) {
             bwg->idx = bwReadIndex(bwg, 0);
             if(!bwg->idx) {
                 fprintf(stderr, "[bwOpen] bwg->idx is NULL bwg->hdr->dataOffset 0x%"PRIx64"!\n", bwg->hdr->dataOffset);

libBigWig/bwValues.h

@@ -1,3 +1,6 @@
+#ifndef LIBBIGWIG_VALUES_H
+#define LIBBIGWIG_VALUES_H
+
 #include <inttypes.h>
 /*! \file bwValues.h
  *
@@ -70,3 +73,5 @@ typedef struct {
     uint8_t type; /**<The block type: 1, bedGraph; 2, variable step; 3, fixed step.*/
     uint16_t nItems; /**<The number of values in a given block.*/
 } bwDataHeader_t;
+
+#endif // LIBBIGWIG_VALUES_H

pyBigWig.c

@@ -197,7 +197,8 @@ char *getNumpyStr(PyArrayObject *obj, Py_ssize_t i) {
 
 //Return 1 if there are any entries at all
 int hasEntries(bigWigFile_t *bw) {
-    if(bw->hdr->nBasesCovered > 0) return 1;
+    if(bw->hdr->indexOffset != 0) return 1;  // No index, no entries pyBigWig issue #111
+    //if(bw->hdr->nBasesCovered > 0) return 1;  // Sometimes headers are broken
     return 0;
 }
 

pyBigWig.h

@@ -2,7 +2,7 @@
 #include <structmember.h>
 #include "bigWig.h"
 
-#define pyBigWigVersion "0.3.17"
+#define pyBigWigVersion "0.3.18"
 
 typedef struct {
     PyObject_HEAD

setup.py

@@ -62,7 +62,7 @@
                     include_dirs = include_dirs)
 
 setup(name = 'pyBigWig',
-       version = '0.3.17',
+       version = '0.3.18',
        description = 'A package for accessing bigWig files using libBigWig',
        author = "Devon P. Ryan",
        author_email = "[email protected]",