various python packages by krafczyk · Pull Request #2320 · spack/spack

krafczyk · 2016-11-12T17:43:53Z

This branch contains a version of the package py-tornado which exposes the problem with the when clauses discussed in #2310.

davydden · 2016-11-12T17:56:51Z

var/spack/repos/builtin/packages/py-tornado/package.py

+    depends_on('py-certifi')
+    depends_on('py-backports-abc', when='^python@:2')
+    depends_on('py-singledispatch', when='^python@:2')
+    depends_on('py-futures', when='+futures^python@:2')


i am not sure, but the :2 could be [...,2), i.e. not including 2. whereas @2: is including 2, i.e. [2,...).

Ranges are inclusive, so this is correct.

ok, did not know that.

davydden · 2016-11-12T17:57:52Z

var/spack/repos/builtin/packages/py-futures/package.py

+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+#
+# This is a template package file for Spack.  We've put "FIXME"


i guess you forgot to remove these

davydden · 2016-11-12T17:58:06Z

var/spack/repos/builtin/packages/py-futures/package.py

+
+
+class PyFutures(Package):
+    """FIXME: Put a proper description of your package here."""


and modify docstring

davydden · 2016-11-12T17:58:16Z

var/spack/repos/builtin/packages/py-futures/package.py

+class PyFutures(Package):
+    """FIXME: Put a proper description of your package here."""
+
+    # FIXME: Add a proper url for your package's homepage here.


and add an url

davydden · 2016-11-12T17:58:26Z

var/spack/repos/builtin/packages/py-monotonic/package.py

+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+#
+# This is a template package file for Spack.  We've put "FIXME"


davydden · 2016-11-12T17:58:35Z

var/spack/repos/builtin/packages/py-monotonic/package.py

+
+
+class PyMonotonic(Package):
+    """FIXME: Put a proper description of your package here."""


davydden · 2016-11-12T17:58:40Z

var/spack/repos/builtin/packages/py-monotonic/package.py

+class PyMonotonic(Package):
+    """FIXME: Put a proper description of your package here."""
+
+    # FIXME: Add a proper url for your package's homepage here.


davydden · 2016-11-12T17:58:49Z

var/spack/repos/builtin/packages/py-singledispatch/package.py

+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+#
+# This is a template package file for Spack.  We've put "FIXME"


davydden · 2016-11-12T17:59:02Z

var/spack/repos/builtin/packages/py-singledispatch/package.py

+
+
+class PySingledispatch(Package):
+    """FIXME: Put a proper description of your package here."""


davydden · 2016-11-12T17:59:06Z

var/spack/repos/builtin/packages/py-singledispatch/package.py

+class PySingledispatch(Package):
+    """FIXME: Put a proper description of your package here."""
+
+    # FIXME: Add a proper url for your package's homepage here.


davydden · 2016-11-12T18:00:34Z

i edited the title, feel free to adjust it if needed.

adamjstewart · 2016-11-12T23:09:41Z

var/spack/repos/builtin/packages/py-jsonschema/package.py

+    extends('python')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-vcversioner')
+    depends_on('py-functools32')


There are a couple other optional dependencies that could be added, but I'm not sure if it really matters:

extras_require = { "format" : ["rfc3987", "strict-rfc3339", "webcolors"], ":python_version=='2.6'": ["argparse", "repoze.lru"], ":python_version=='2.7'": ["functools32"], }

adamjstewart · 2016-11-12T23:12:16Z

var/spack/repos/builtin/packages/py-pycurl/package.py

+
+    extends('python')
+    depends_on('py-setuptools', type='build')
+    depends_on('curl')


If you want to be more specific about the dependency versions, they are:

Requirements ------------ - Python 2.6, 2.7 or 3.1 through 3.5. - libcurl 7.19.0 or better.

Added in 1ae60bb.

adamjstewart · 2016-11-12T23:14:12Z

var/spack/repos/builtin/packages/py-singledispatch/package.py

+    extends('python')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six')


py-ordereddict is also required for Python versions less than 2.7.

Added in a111742.

adamjstewart · 2016-11-12T23:17:42Z

var/spack/repos/builtin/packages/py-tornado/package.py

+    depends_on('py-futures', when='+futures^python@:2')
+    depends_on('py-monotonic', when='+monotonic^python@:2')
+    depends_on('py-pycurl', when='+curl')
+    depends_on('py-twisted', when='+twisted')


The setup.py doesn't mention integrating with py-futures through py-twisted. Where do they come from?

I added those since they're listed as optional dependencies in the Arch py-tornado package. I'm looking into it.

If you look at this page: http://www.tornadoweb.org/en/stable/index.html They list these packages under prerequisites as 'optional'. I'll leave them off for now since I just want to get things working.

adamjstewart · 2016-11-12T23:20:29Z

var/spack/repos/builtin/packages/py-tornado/package.py

+    depends_on('py-setuptools', type='build')
+    depends_on('py-certifi')
+    depends_on('py-backports-abc', when='^python@:2')
+    depends_on('py-singledispatch', when='^python@:2')


[email protected]: is needed for Python < 3.5
py-singledispatch and py-certifi are needed for Python < 3.4
py-ordereddict is needed for Python < 2.7
py-backports is needed for Python < 2.7.9

See setup.py for details.

Corrected this in d5ed437, Also added backports.ssl_match_hostname.

adamjstewart · 2016-11-12T23:23:09Z

var/spack/repos/builtin/packages/py-zmq/package.py

+
+    extends('python')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cython')


Requires [email protected]:, py-py, and py-cffi

Now done in 951c82e

adamjstewart · 2016-11-12T23:25:52Z

var/spack/repos/builtin/packages/py-futures/package.py

+
+    # FIXME: Add a proper url for your package's homepage here.
+    homepage = "http://www.example.com"
+    url      = "https://pypi.python.org/packages/55/db/97c1ca37edab586a1ae03d6892b6633d8eaa23b23ac40c7e5bbc55423c78/futures-3.0.5.tar.gz"


For url's like this where the PyPi link contains the hash of the package, things like spack versions and spack checksum won't work. Can you try out the pypi.io link format suggested in #1939 (comment)?

I've corrected all of the packages I've added. However, there are a number of other packages which need this as well, and there's still the issue of #2335.

krafczyk · 2016-11-14T00:41:24Z

@adamjstewart @davydden I will work on all of these issues, however the purpose of this branch is to show the when clause errors. My branch features/numerous_py_packages will contain the changes suggested here. I'm creating a pull request for that branch as well.

davydden · 2016-11-14T08:13:29Z

@krafczyk i would say it's better to keep everything in one branch and since @adamjstewart already commented a lot, it would be easier if you just push your changes here. I don't see a reason for another branch with the same content.

davydden · 2016-11-16T20:07:14Z

@krafczyk : looking at commits, something is wrong here (same commits have different hashes and are duplicated). I suggest you (i) reset your local branch to 7d18593; (ii) rebase on top of current develop in Spack (don't forget ot fetch it or pull it if it's your local copy); (iii) cherry-pick 3f0a6e1 and 3bf1d9b.

This should give you a clean local branch. If all looks good, you can then git push --force to your remote on GitHub. If something went south, you can always git reset --hard to the remote branch on Github.

krafczyk · 2016-11-16T20:51:03Z

@davydden : I've done what you suggested. I'll pay closer attention next time.

davydden · 2016-11-16T20:52:34Z

@krafczyk thanks, looks nice now 👍

krafczyk · 2016-11-17T21:46:52Z

@adamjstewart, @davydden, @citibeth, @jppelteret: I've nearly finished adding everything necessary for the jupyter-notebook to work. Now I'm running into a strange problem having to do with npm.

Since I'm not that familiar with npm, perhaps one of you can help me out here.

When I try to install py-jupyter_notebook from 0d36e3d, I get the output located at this pastebin: http://pastebin.com/rt1Ghv4Z

The log file from the build is at this pastebin: http://pastebin.com/fZR4a8z1

So, while the correct node is used along with the correct npm, I'm getting weird access errors, and npm is trying to write to my home directory. I would think ideally that anything npm installs ought to belong to the py-jupyter_notebook prefix. I'm not sure how to make that happen though.

citibeth · 2016-11-17T22:49:34Z

Sigh, yet another package manager with its own ideas of how to do things
that breaks spack. You need to figure out how to install jupyter without
npm. Or trick npm by setting a fake home directory.
On Nov 17, 2016 4:47 PM, "Matthew Scott Krafczyk" [email protected]
wrote:

@adamjstewart https://github.com/adamjstewart, @davydden
https://github.com/davydden, @citibeth https://github.com/citibeth,
@jppelteret https://github.com/jppelteret: I've nearly finished adding
everything necessary for the jupyter-notebook to work. Now I'm running into
a strange problem having to do with npm.

Since I'm not that familiar with npm, perhaps one of you can help me out
here.

When I try to install py-jupyter_notebook from 0d36e3d
0d36e3d,
I get the output located at this pastebin: http://pastebin.com/rt1Ghv4Z

The log file from the build is at this pastebin:
http://pastebin.com/fZR4a8z1

So, while the correct node is used along with the correct npm, I'm getting
weird access errors, and npm is trying to write to my home directory. I
would think ideally that anything npm installs ought to belong to the
py-jupyter_notebook prefix. I'm not sure how to make that happen though.

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
#2320 (comment), or mute
the thread
https://github.com/notifications/unsubscribe-auth/AB1cdwm6NjPgvy9S0g7hRhSaOHPDD0sxks5q_MtOgaJpZM4Kwek5
.

krafczyk · 2016-11-18T16:25:55Z

Is there a way to set environment variables when installing or using a specific package?
If there is, is there a way to append like what goes on in PATH?

tgamblin · 2016-11-18T16:31:10Z

@krafczyk: See the section on setup_dependent_environment. You can customize what goes in the build environment of dependents, and in the run environment of things that use a package.

davydden · 2016-11-18T16:32:51Z

@krafczyk you can also set environment by os.environ['SLEPC_DIR'] = os.getcwd() or alike.

krafczyk · 2016-11-18T16:35:39Z

Great!

tgamblin · 2016-11-18T16:45:50Z

@krafczyk: note that if you modify os.environ inside setup_dependent_environment, that will succeed for modifying the build environment, because setup_dependent_environment runs for every dependency of a package before it is built. However, it won't get things into a package's module file -- run_env does that. spack_env is provided as a convenience so that the API for setting up the build environment is the same as the one for the run environment.

There is perhaps better documentation on this in the module configuration section.

davydden · 2016-11-19T00:07:38Z

var/spack/repos/builtin/packages/flex/package.py

+    url = "https://github.com/westes/flex/releases/download/v2.6.2/flex-2.6.2.tar.gz"

-    version('2.6.0', '5724bcffed4ebe39e9b55a9be80859ec')
-    version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde')


why removing 2.5.39 and 2.6.0 ? 2.5.39 is need by foam-extend, for example. Removing versions is generally not a good idea.

btw, the old download works fine for me (i checked 2.5.39). Also if that is not needed for python packages, then please create a separate PR for this change.

Sorry about that, I've fixed up flex good and proper this time.

The reason I did that was because I was running into a segfault when building binutils and moving to the latest version of flex (2.6.2) seemed to solve the problem. In addition, flex development has moved to github so It would be good to reflect that change. The md5s have all been updated.

binutils is part of the dependency chain for yt which was my ultimate goal for using jupyter-notebook.

@davydden, I've created #2385 to deal with this commit. I've also rebased this branch and removed the flex commits.

krafczyk · 2016-11-19T00:52:53Z

I'd like to announce that jupyter-notebook is now working as expected for me! It took a lot of work, but now I'm able to use yt in jupyter-notebook!

About the npm problem, it turns out that npm was trying to write to the 'cache' which was set to ~/.npm. This can be overridden with the environment variable npm_config_cache, so I've set this to the npm prefix. This means that all npm downloads will go into npm's prefix. This is a kludgy fix, but it seems to work for now.

There are quite a few commits, so I'd like comments from folks.

citibeth · 2016-11-19T03:01:53Z

The npm thing means that npm downloads cannot be versioned independently of
npm itself or of each other. I suppose the truly right way to do this
(other than installing npm downloads correctly as with the rest of Spack)
would be to put them all the the Jupyter prefix.

On Fri, Nov 18, 2016 at 7:52 PM, Matthew Scott Krafczyk <
[email protected]> wrote:

I'd like to announce that jupyter-notebook is now working as expected for
me! It took a lot of work, but now I'm able to use yt in jupyter-notebook!

About the npm problem, it turns out that npm was trying to write to the
'cache' which was set to ~/.npm. This can be overridden with the
environment variable npm_config_cache, so I've set this to the npm prefix.
This means that all npm downloads will go into npm's prefix. This is a
kludgy fix, but it seems to work for now.

There are quite a few commits, so I'd like comments from folks.

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
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.

citibeth · 2017-01-05T17:41:04Z

I believe it will be squashed when it's merged.

…

On Thu, Jan 5, 2017 at 12:30 PM, Matthew Scott Krafczyk < ***@***.***> wrote: @davydden <https://github.com/davydden>: I've removed the FIXME's you mentioned @adamjstewart <https://github.com/adamjstewart>: I've fixed the grammar issues you raised as well as changed the package names you mentioned. Do you guys think I should squash all these changes into one commit? as it stands there are almost 100 commits of work here. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2320 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB1cd7r7bN2nExIAJyhEeIWQrX5UiU4hks5rPSiigaJpZM4Kwek5> .

adamjstewart · 2017-01-05T17:47:08Z

var/spack/repos/builtin/packages/py-ipython_genutils/package.py

@@ -0,0 +1,42 @@
+##############################################################################


This one still needs to be renamed.

adamjstewart · 2017-01-05T17:51:24Z

var/spack/repos/builtin/packages/node-js/package.py

+                                            stdout=subprocess.PIPE)
+            result_which = process_pipe.communicate()[0]
+            process_pipe = subprocess.Popen(["whereis", "libtool"], 
+                                            stdout=subprocess.PIPE)


You ought to be able to use which('libtool'), but I'm fine with merging this as is.

adamjstewart · 2017-01-05T17:53:06Z

var/spack/repos/builtin/packages/py-widgetsnbextension/package.py

+
+    depends_on('py-setuptools', type='build')
+    depends_on('[email protected]:2.7.999,3.3:')
+    depends_on('[email protected]:')


Last one, I think.

davydden · 2017-01-05T17:53:22Z

I would not squash it even during the merge as commits have different authorship

tgamblin · 2017-01-05T18:18:19Z

@alalazo:

Does pulling #2748 solve the issue with the tests?

Yep! Perfect!

tgamblin · 2017-01-05T18:22:57Z

@adamjstewart: approve?

krafczyk · 2017-01-05T18:33:23Z

@tgamblin, I did not know that you could make a commit on my fork without me pulling it. Nifty!

tgamblin · 2017-01-05T18:35:15Z

@krafczyk: There's a checkbox for this when you commit the PR -- it's the allow edits by maintainers one.

Adds the following packages: node-js py-backports-abc py-functools32 py-pycurl py-vcversione npm py-certifi py-jsonschema py-tornado py-zmq - Added python packages that are dependencies for the Jupyter suite - Update new python packaages to use extension package install function. - Added npm and node-js packages

This adds the following packages: py-backports-shutil-get-terminal-size py-nbformat py-backports-ssl-match-hostname py-pathlib2 py-entrypoints py-pickleshare py-futures py-pip py-ipykernel py-prompt-toolkit py-ipython-genutils py-ptyprocess py-ipywidgets py-simplegeneric py-jupyter-client py-singledispatch py-jupyter-console py-terminado py-jupyter-core py-traitlets py-jupyter-notebook py-wcwidth py-monotonic py-widgetsnbextension py-nbconvert

tgamblin · 2017-01-05T18:39:49Z

I squashed this into two commits by @jppelteret and @krafczyk. They now list the added packages:

$ spack pkg diff develop HEAD^
HEAD^:
    node-js  py-backports-abc  py-functools32  py-pycurl   py-vcversioner
    npm      py-certifi        py-jsonschema   py-tornado  py-zmq

$ spack pkg diff HEAD^ HEAD
HEAD:
    py-backports-shutil-get-terminal-size  py-nbformat
    py-backports-ssl-match-hostname        py-pathlib2
    py-entrypoints                         py-pickleshare
    py-futures                             py-pip
    py-ipykernel                           py-prompt-toolkit
    py-ipython-genutils                    py-ptyprocess
    py-ipywidgets                          py-simplegeneric
    py-jupyter-client                      py-singledispatch
    py-jupyter-console                     py-terminado
    py-jupyter-core                        py-traitlets
    py-jupyter-notebook                    py-wcwidth
    py-monotonic                           py-widgetsnbextension

@krafczyk: if the tests pass and you're ok with this we can merge.

krafczyk · 2017-01-05T18:41:36Z

@tgamblin I'm testing that things still work for me as I expect. I'll let you know in a bit.

tgamblin · 2017-01-05T18:45:32Z

@krafczyk: Sounds good. If you need to revert, the tip before rebasing was b6edd93. The only diff between that and the two squashed commits above is that the squashed ones are based on develop with @alalazo's test fix.

$ git co fix/when_variants_plus_dependency 
Switched to branch 'fix/when_variants_plus_dependency'
Your branch is up-to-date with 'krafczyk/fix/when_variants_plus_dependency'.
$ git diff b6edd93
diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py
index 11127d8..79d9018 100644
--- a/lib/spack/spack/test/conftest.py
+++ b/lib/spack/spack/test/conftest.py
@@ -122,7 +122,6 @@ def builtin_mock(repo_path):
 def refresh_builtin_mock(builtin_mock, repo_path):
     """Refreshes the state of spack.repo"""
     # Get back the real repository
-    spack.repo.swap(builtin_mock.real)
     mock_repo = copy.deepcopy(repo_path)
     spack.repo.swap(mock_repo)
     return builtin_mock

krafczyk · 2017-01-05T18:53:52Z

@tgamblin: Everything looks good to me. You can merge when the tests are finished.

adamjstewart · 2017-01-05T19:28:04Z

@tgamblin @alalazo Any idea why the macOS tests take so much longer?

alalazo · 2017-01-05T19:36:50Z

@adamjstewart It's the set-up phase that seems to take a lot (e.g brew update & Co.).

krafczyk · 2017-01-05T21:16:27Z

@tgamblin tests are done, ready to merge

tgamblin · 2017-01-06T00:11:03Z

@krafczyk: merged! Thanks a lot to you and @jppelteret!

davydden added python WIP labels Nov 12, 2016

davydden reviewed Nov 12, 2016

View reviewed changes

davydden changed the title ~~Fix/when variants plus dependency~~ various python packages Nov 12, 2016

adamjstewart reviewed Nov 12, 2016

View reviewed changes

krafczyk force-pushed the fix/when_variants_plus_dependency branch from 8ade5b2 to 2d5aa0c Compare November 15, 2016 21:49

krafczyk force-pushed the fix/when_variants_plus_dependency branch from 15ffe16 to a111742 Compare November 16, 2016 20:49

davydden suggested changes Nov 19, 2016

View reviewed changes

adamjstewart reviewed Jan 5, 2017

View reviewed changes

adamjstewart approved these changes Jan 5, 2017

View reviewed changes

jppelteret and others added 2 commits January 5, 2017 10:37

tgamblin force-pushed the fix/when_variants_plus_dependency branch from b6edd93 to 126a115 Compare January 5, 2017 18:38

tgamblin merged commit 8c65030 into spack:develop Jan 6, 2017

tgamblin mentioned this pull request Jan 6, 2017

various python package version and dependency updates #2751

Merged

krafczyk deleted the fix/when_variants_plus_dependency branch January 6, 2017 02:37

adamjstewart added a commit that referenced this pull request Jan 8, 2017

Redo changes from #2320 that were lost in rebase

eff5d1d

adamjstewart mentioned this pull request Jan 8, 2017

PythonPackage class #2778

Merged

adamjstewart added a commit that referenced this pull request Jan 8, 2017

Convert packages from #2320 to PythonPackage, fix deptypes

9b2326e

This was referenced Jan 9, 2017

Add Jupyter-related Python Packages #2122

Closed

Added npm and node-js packages #2128

Closed

Adding the py-ipdb package for more stable debugging with iPython. #2824

Merged



		class PyFutures(Package):
		"""FIXME: Put a proper description of your package here."""



		class PyMonotonic(Package):
		"""FIXME: Put a proper description of your package here."""



		class PySingledispatch(Package):
		"""FIXME: Put a proper description of your package here."""

		@@ -0,0 +1,42 @@
		##############################################################################

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krafczyk commented Nov 12, 2016

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davydden commented Nov 12, 2016

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krafczyk Nov 16, 2016 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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krafczyk commented Nov 14, 2016 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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krafczyk Nov 16, 2016 •

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krafczyk commented Nov 14, 2016 •

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