Merge branch 'master' of github.com:ContinuumIO/conda

CHANGELOG.txt

@@ -1,8 +1,14 @@
-2013-XX-XX   1.5.1:
+2013-XX-XX   1.5.2:
+-------------------
+  * fixed issue 59: bad error message when pkgs dir is not writable
+
+
+2013-04-19   1.5.1:
 -------------------
   * fixed issue 71 and (73 duplicate): not being able to install packages
     starting with conda (such as 'conda-api')
   * fixed issue 69 (not being able to update Python / NumPy)
+  * fixed issue 76 (cannot install mkl on OSX)
 
 
 2013-03-22   1.5.0:

conda/builder/index.py

@@ -1,11 +1,12 @@
 import os
+import bz2
 import json
 import base64
 import hashlib
 import tarfile
 from os.path import join, getmtime
 
-from utils import bzip2, file_info
+from utils import file_info
 
 
 app_meta_path_fmt = 'App/%(name)s/meta.json'
@@ -31,6 +32,17 @@ def read_index_tar(tar_path):
             add_app_metadata(t, info)
         return info
 
+def write_repodata(repodata, dir_path):
+    data = json.dumps(repodata, indent=2, sort_keys=True)
+    # strip trailing whitespace
+    data = '\n'.join(line.rstrip() for line in data.split('\n'))
+    # make sure we have newline at the end
+    if not data.endswith('\n'):
+        data += '\n'
+    with open(join(dir_path, 'repodata.json'), 'w') as fo:
+        fo.write(data)
+    with open(join(dir_path, 'repodata.json.bz2'), 'wb') as fo:
+        fo.write(bz2.compress(data))
 
 def update_index(dir_path, verbose=False, force=False):
     if verbose:
@@ -77,8 +89,8 @@ def update_index(dir_path, verbose=False, force=False):
             except KeyError:
                 pass
 
-    repodata = {'packages': index, 'icons': icons, 'info': {}}
-    repodata_path = join(dir_path, 'repodata.json')
-    with open(repodata_path, 'w') as fo:
-        json.dump(repodata, fo, indent=2, sort_keys=True)
-    bzip2(repodata_path)
+    repodata = {'packages': index, 'info': {}}
+    if icons:
+        repodata['icons'] = icons
+
+    write_repodata(repodata, dir_path)

conda/builder/utils.py

@@ -1,4 +1,3 @@
-import bz2
 import sys
 import hashlib
 import platform
@@ -21,17 +20,6 @@ def rel_lib(f):
         return normpath(f.count('/') * '../') + '/lib'
 
 
-def bzip2(path, verbose=False):
-    bz2path = path + '.bz2'
-    if verbose:
-        print "bz2ing:", path
-    with open(path, 'rb') as fi:
-        data = fi.read()
-    data = bz2.compress(data)
-    with open(bz2path, 'wb') as fo:
-        fo.write(data)
-
-
 def md5_file(path):
     with open(path, 'rb') as fi:
         h = hashlib.new('md5')

conda/remote.py

@@ -62,39 +62,60 @@ def fetch_file(url, fn, md5=None, size=None, progress=None,
     for x in range(retries):
         try:
             fi = urllib2.urlopen(url + fn)
-            log.debug("fetching: %s [%s]" % (fn, url))
-            n = 0
-            h = hashlib.new('md5')
-            if size is None:
-                length = int(fi.headers["Content-Length"])
-            else:
-                length = size
+        except IOError:
+            log.debug("Attempt %d failed at urlopen" % x)
+            continue
+        log.debug("Fetching: %s [%s]" % (fn, url))
+        n = 0
+        h = hashlib.new('md5')
+        if size is None:
+            length = int(fi.headers["Content-Length"])
+        else:
+            length = size
+
+        if progress:
+            progress.widgets[0] = fn
+            progress.maxval = length
+            progress.start()
+
+        need_retry = False
 
+        try:
+            fo = open(pp, 'wb')
+        except IOError:
+            raise RuntimeError("Could not open %r for writing.  "
+                         "Permissions problem or missing directory?" % pp)
+        while True:
+            try:
+                chunk = fi.read(16384)
+            except IOError:
+                log.debug("Attempt %d failed at read" % x)
+                need_retry = True
+                break
+            if not chunk:
+                break
+            try:
+                fo.write(chunk)
+            except IOError:
+                raise RuntimeError("Failed to write to %r." % pp)
+            if md5:
+                h.update(chunk)
+            n += len(chunk)
             if progress:
-                progress.widgets[0] = fn
-                progress.maxval = length
-                progress.start()
-
-            with open(pp, 'wb') as fo:
-                while True:
-                    chunk = fi.read(16384)
-                    if not chunk:
-                        break
-                    fo.write(chunk)
-                    if md5:
-                        h.update(chunk)
-                    n += len(chunk)
-                    if progress:
-                        progress.update(n)
-
-            fi.close()
-            if progress: progress.finish()
-            if md5 and h.hexdigest() != md5:
-                raise RuntimeError("MD5 sums mismatch for download: %s" %
-                                   fn)
+                progress.update(n)
+
+        fo.close()
+        if need_retry:
+            continue
+
+        fi.close()
+        if progress: progress.finish()
+        if md5 and h.hexdigest() != md5:
+            raise RuntimeError("MD5 sums mismatch for download: %s" % fn)
+        try:
             os.rename(pp, path)
-            return url
-        except IOError:
-            log.debug('download failed try: %d' % x)
+        except OSError:
+            raise RuntimeError("Could not rename %r to %r." % (pp, path))
+        return url
 
     raise RuntimeError("Could not locate file '%s' on any repository" % fn)

docs/source/examples/depends.rst

@@ -8,130 +8,96 @@ for a given package.
 
 .. code-block:: bash
 
-    $ conda depends numpy
-    numpy depends on the following packages:
-        nose 1.1.2
-        python 2.7
-        readline 6.2
-        sqlite 3.7.13
-        zlib 1.2.7
+    $ conda depends scipy
+    scipy depends on the following packages:
+        nose-1.2.1
+        numpy-1.7.0
+        python-2.7.3
+        readline-6.2
+        sqlite-3.7.13
+        tk-8.5.13
+        zlib-1.2.7
 
 To check a package dependency in a specific named environment in /anaconda/envs, the name option (``-n``) is used.
 
 .. code-block:: bash
 
-    $ conda depends -n foo numpy
-        numpy depends on the following packages:
-        nose-1.1.2
+    $ conda depends -n foo scipy
+    scipy depends on the following packages:
+        nose-1.2.1
+        numpy-1.7.0
         python-2.7.3
         readline-6.2
         sqlite-3.7.13
+        tk-8.5.13
         zlib-1.2.7
 
 Running ``conda depends`` with the prefix option (``-p``) checks a specified packages dependencies within an Anaconda environment
 located at a given path.
 
 .. code-block:: bash
 
-    $ conda depends -p ~/anaconda/envs/foo/ numpy
-        numpy depends on the following packages:
-        nose-1.1.2
+    $ conda depends -p ~/anaconda/envs/foo/ scipy
+    scipy depends on the following packages:
+        nose-1.2.1
+        numpy-1.7.0
         python-2.7.3
         readline-6.2
         sqlite-3.7.13
+        tk-8.5.13
         zlib-1.2.7
 
     
 Running ``conda depends`` with the reverse dependency command shows all packages that require NumPy.
 
 .. code-block:: bash
 
-    $ conda depends -r numpy
-    The following activated packages depend on numpy:
-        h5py-2.0.1
-        iopro-1.1.0
-        matplotlib-1.1.1
-        numba-0.1.1
-        numbapro-0.6
-        numexpr-2.0.1
-        pandas-0.8.1
-        pysal-1.4.0
-        pytables-2.4.0
-        scikit-learn-0.11
-        scikits-image-0.6.1
-        scipy-0.11.0
+    $ conda depends -r scipy
+    The following activated packages depend on scipy:
+        accelerate-1.0.1
+        pandas-0.10.1
+        pysal-1.5.0
+        scikit-learn-0.13
         statsmodels-0.4.3
-        wiserf-0.9
+        wiserf-1.1
 
-Using reverse dependency in addition to the verbose (``-v``) and ``no-prefix`` commands offers
+Using reverse dependency in addition to the verbose (``-v``) commands offers
 more information and includes packages that depend on any version of NumPy.
 
 .. code-block:: bash
 
-    $ conda depends --no-prefix -rv numpy
-    The following packages depend on numpy:
-        chaco-4.2.1.dev-np17py27_0
-        h5py-2.0.1-np17py26_0
-        h5py-2.0.1-np17py27_0
-        h5py-2.1.0-np17py26_0
-        h5py-2.1.0-np17py27_0
-
-        ....
-
-        statsmodels-0.4.3-np16py26_0
-        statsmodels-0.4.3-np16py27_0
-        statsmodels-0.4.3-np17py26_0
+    $ conda depends -rv scipy
+    The following activated packages depend on scipy:
+        accelerate-1.0.1-np17py27_p0
+        pandas-0.10.1-np17py27_0
+        pysal-1.5.0-np17py27_0
+        scikit-learn-0.13-np17py27_0
         statsmodels-0.4.3-np17py27_0
-        wiserf-0.9-np17py27_0
-
-``conda depends`` with just ``--no-prefix -r`` shows us any version of NumPy's dependencies in a more easily parsed
-form, showing how many versions of NumPy can be used to build that specific package.
+        wiserf-1.1-np17py27_1
 
-.. code-block:: bash
-
-    $ conda depends --no-prefix -r numpy
-    The following packages depend on numpy:
-        chaco-4.2.1.dev
-        h5py-2.0.1 (2 builds)
-        h5py-2.1.0 (2 builds)
-        iopro-1.0 (2 builds)
-        iopro-1.1.0 (2 builds)
-        iopro-1.2rc1 (2 builds)
-
-        ....
-
-        pytables-2.4.0 (4 builds)
-        scikit-learn-0.11 (13 builds)
-        scikits-image-0.6.1 (6 builds)
-        scipy-0.11.0 (3 builds)
-        scipy-0.11.0rc2 (3 builds)
-        statsmodels-0.4.3 (4 builds)
-        wiserf-0.9
 
 Adding the ``MAX_DEPTH`` command allows greater control over how many levels 
 deep conda's dependency list will go.  By default, it is set to 0, but
 for the purposes of demonstration, it is made explicit here.
 
 .. code-block:: bash
 
-    $ conda depends -rm 0 sqlite
-    The following activated packages depend on sqlite:
-        anaconda-launcher-0.0
-        bitarray-0.8.0
-        bitey-0.0
-        conda-1.0
-        cython-0.17.1
-        dateutil-1.5
-        flask-0.9
-        gevent-0.13.7
-        gevent-websocket-0.3.6
-        
-        ....
-
-        sympy-0.7.1
-        tornado-2.3
-        werkzeug-0.8.3
-        wiserf-0.9
+$ conda depends -rm 0 sqlite
+The following activated packages depend on sqlite:
+    _license-1.1
+    accelerate-1.0.1
+    astropy-0.2
+    biopython-1.60
+    bitarray-0.8.1
+    bitey-0.0
+    boto-2.6.0
+    chaco-4.2.1.dev
+    cubes-0.10.2
+    ...
+    werkzeug-0.8.3
+    wiserf-1.1
+    xlrd-0.9.0
+    xlwt-0.7.4
 
 In this example, setting the ``MAX_DEPTH`` to 1 shows only the packages 
 that depend on sqlite, while not displaying what these packages depend