Hi guys, the latest sync of your fork with Galaxy stable was on 2013-02-08, according to: https://bitbucket.org/galaxycloud/galaxy/commits/all?page=10
This is the diff of fetch_eggs.py in between your version and galaxy-central: https://gist.github.com/martenson/f5bc887b1721732991e0 It doesn't look like there is something that may be affecting the problem. M. On Wed Feb 04 2015 at 8:31:08 PM Stephen Rosen <siro...@uchicago.edu> wrote: > Hi Nate, > > Thanks so much for helping me out with this. > > It seems that I've miscommunicated what I'm doing a little bit. > I'm installing a package from that git repo using pip separately from > running the galaxy setup script. > That is, I want to install a python package and I want to setup galaxy as > two separate (and ideally independent) steps in my script. > I have no desire to do anything particularly esoteric or clever with > Galaxy's eggs or to install them myself. > Somehow, doing a pip install of my desired package is breaking the later > run of fetch_eggs.py > > If I understand you correctly, fetch_eggs.py can hit conflicts with > site-packages, but is misreporting them as EggNotFetchable. > I am aware that we're using a fork of the Galaxy source ( > https://bitbucket.org/galaxycloud/galaxy/src ), so it may be that we have > an outdated of fetch_eggs.py which carries a bug that has since been > patched. > Sorry for not mentioning it earlier -- it slipped my mind that we're > probably trailing behind the modern Galaxy default head. > > If I put in the extra legwork now to wrap Galaxy in a virtualenv, this > issue will presumably disappear, but that assumes that I don't want to add > any packages to the python used for the uwsgi process. > I'll have to ask folks on the Globus Genomics team whether or not that is > needed -- I certainly hope not, since it means that there is some packaging > conflict we need to resolve. > The only reason I haven't done so already is time constraint -- I've been > trying to get this install scripting done as quickly as possible without > compromising anything truly needful. > > > All the same, I'll take some time tomorrow to provision a fresh server and > generate the stacktrace for you. > I'll also take some time to test with the latest Galaxy source, to see if > I get different behavior. > In the best case, this bug no longer exists for the modern source, but in > the worst case it bears the attention. > > > I don't have any sense of the reliability of fetch_eggs.py and company -- > my experience has been of a particular bug that presented on my first > contact with these scripts, so naturally I have a bias against them. > That said, I think the Python community may have finally settled on a > package manager, even if we can't seem to agree on a package format or > tooling surrounding it. > That's just an opinion though -- I have no blog post from Guido to back it > up. > > > I was not aware of the UCS2 vs. UCS4 issue -- thanks very much for the > citations, very helpful in understanding the problem space. > > Thanks, > -Stephen > > On Wed, Feb 4, 2015 at 5:41 PM, Nate Coraor <n...@bx.psu.edu> wrote: > >> Hi Stephen, >> >> I'll try to reply as in-depth as I can. >> >> On Wed, Feb 4, 2015 at 1:41 PM, Stephen Rosen <siro...@uchicago.edu> >> wrote: >> >>> Hi Galaxy Dev, >>> >>> I've been looking at the setup scripts for Galaxy to try to understand a >>> problem I recently had provisioning a Galaxy server. >>> I will readily admit that I have not read all of the relevant code >>> top-to-bottom, but I have at least skimmed all of it and read much of it. >>> Sorry if these questions are answered somewhere in Trello, the Wiki, or >>> somewhere else, but I was not able to find answers in any public locations. >>> >>> As a small bit of probably irrelevant context: >>> I'm working with the Globus Genomics group on the DevOps side of things. >>> We're using Chef. >>> I've only just started working with the group in the past couple of >>> weeks (so my expertise with Galaxy itself is limited to nonexistent). >>> >>> >>> First, to describe the problem: >>> >>> >>> We want to provision a server running Galaxy without explicitly wrapping >>> it in a virtualenv. >>> Unless I missed something, that means that it's using system python. >>> When we use pip to install a package from a git repository before >>> running the setup scripts, fetch_eggs fails saying it failed to fetch >>> WebError 0.8a >>> If we install the same package from git with `pip install --egg ...` we >>> get a hunky-dory system where everything seems to work. >>> >> >> A virtualenv is itself just a wrapper around whichever python binary was >> used to create it. I'd still suggest using a virtualenv created with the >> system python unless you have a really strong reason not to. In fact, I'm >> working on Galaxy process management and a command line tool for that >> management that will automatically create and use a virtualenv going >> forward. >> >> I'm a bit confused at what's happening here - you mention installing a >> package from a git repository with pip, but then refer to Galaxy's >> fetch_eggs(.py) script, which doesn't use pip or git. >> >> >>> As far as I can tell, there is no reason that this should be the case. >>> Sure, putting the git source directly into site-packages might cause >>> issues upon installation, but EggNotFetchable exceptions should only be >>> thrown if the egg actually can't be pulled down from eggs.g2.bx.psu.edu >>> , right? >>> >> >> EggNotFetchable can be thrown if you happen to be using a platform for >> which we do not provide eggs, although those are fairly uncommon. Right now >> we should cover x86/x86_64 Linux and any flavor of Intel OS X after 10.5. >> >> >>> I don't feel comfortable trying to make further progress on my >>> provisioning scripts without knowing why this is happening. >>> I'd hate to be bitten by this later on in the process. >>> >>> Yes, the package in question may have poor behavior (likely it does), >>> but that doesn't change the fact that the error is totally misleading. >>> Furthermore, it doesn't appear that this poor behavior impedes me from >>> doing a pip install of the WebError package or any other packages from PyPI. >>> >>> In case someone else wants to test to replicate, this is the command >>> being used: >>> pip install --egg git+ >>> https://github.com/globusonline/python-nexus-client@599f04edef6b72569b7a5b272b0b847dcda3ea99#egg=nexus-client >>> problems occur if you omit `--egg`. >>> >> >> None of this process is using Galaxy's egg handling, so I am not sure >> where the EggNotFetchable is coming from. What command are you running to >> get an EggNotFetchable error. >> >> >>> Second, a question about the rationale for Galaxy's egg handling: >>> >>> >>> Why is all of this wrapped up in these scripts in the first place? >>> I understand that pip might not be present on every platform, and I >>> don't mean to question a decision to support systems without it. >>> However, as detailed below, Galaxy does not support any platforms which >>> are incapable of running pip. >>> >> >> This isn't the case - Galaxy does not use pip to install the framework >> dependencies at all. Some tool dependencies installed from the Tool Shed do >> use pip, but that's entirely separate from the dependencies of the Galaxy >> application. >> >> The `scripts/scramble.py` script can be used to automatically build eggs >> on platforms which we do not prebuild eggs for. If this is necessary, >> `scripts/fetch_eggs.py` should tell you. >> >> >>> Furthermore, pip is being pushed by the Python maintainers over >>> easy_install, so it's not like there isn't a clear choice in terms of which >>> one to support. >>> >>> Perhaps most importantly, there don't appear to be any clear-cut options >>> to do the following, which I would consider a more ordinary workflow: >>> >>> - Run a galaxy script (like check_eggs) to generate a list of packages >>> from eggs.g2.bx.psu.edu for platform (redirect output to >>> requirements.txt or similar) >>> - `pip install -r requirements.txt` >>> >> >> This is exactly what `scripts/check_eggs.py` and `scripts/fetch_eggs.py` >> do. >> >> There are 3 reasons for the way we handle eggs in Galaxy: >> >> 1. Galaxy has a huge (and ever-growing) list of dependent python modules >> with C extensions. If we did not prebuild and distribute eggs for these, >> the initial setup to get Galaxy running would be long and problematic. Some >> people who download Galaxy to develop tools may not even have compilers >> installed, let alone the multitude of -dev or -devel packages that aren't >> part of a default Debian or RHEL installation that would be required to >> build all of these packages from source. One of the things that I feel >> makes Galaxy so accessible is that you can start using it immediately after >> you clone the source. So that ability to clone and start and have it work >> as reliably (and quickly) as possible is a high priority. >> >> 2. Galaxy started using eggs in 2005 or 2006. At this time, everything >> used distutils. pkg_resources came around, which soon brought setuptools >> and easy_install. After this came distutils2, pip and finally, these days, >> wheels. Our need for binary dependency packaging predated almost all of >> these (in fact, most packages in these days didn't even install .egg-info, >> which was the only reliable way to know what version of a module you were >> using) and as each new iteration of packaging/management came along it was >> never clear that any of them had "won" (and in fact, most of them lost). On >> top of this, the Python packaging folks have known for years that Python's >> platform detection for binary compatibility is broken[1]. While I was >> assured it'd be fixed soon, even with a complete reimplementation of Python >> packaging (wheels), they still haven't even made an effort to fix this >> problem[2]. In fact, binary wheels for Linux are explicitly not allowed on >> PyPI because of this. >> >> 3. We tightly control the versions of all of our dependencies, which is >> not always possible with pip if you aren't also controlling the source of >> your packages. >> >> [1] >> https://mail.python.org/pipermail/distutils-sig/2010-January/015345.html >> [2] http://lucumr.pocoo.org/2014/1/27/python-on-wheels/ >> >> The above could be part of a galaxy provisioning script, rather than >>> exposed to the administrator. >>> >>> That also makes it significantly easier to control and manage the >>> virtualenv in which we run Galaxy, since we don't have to worry about >>> egg-related logic that we don't control and we know that the virtualenv's >>> bin dir will be earlier in the PATH than the system pip's dir. >>> Yes, I said above that our setup is presently using system python -- >>> switching to a virtualenv is one of the many items on my to-do list. >>> In fact, I would expect that the default, desired setup for Galaxy would >>> be to put it in a virtualenv, rather than using system python, and to use >>> pip, rather than fetch_eggs.py and company. >>> >> >> A virtualenv is indeed the strongly preferred setup as I mentioned above. >> However, Galaxy does not install its eggs to the virtualenv. The virtualenv >> is there to avoid conflicts with things in the default python's >> site-packages/dist-packages. Galaxy's eggs are installed to (by default) >> the `eggs/` directory in the Galaxy source. >> >> However, the problem, as I now see it, is that you are trying to install >> all of Galaxy's dependencies, even at their correct versions, using pip, >> rather than letting Galaxy handle its eggs as it does. This is not going to >> work, Galaxy is going to insist on using its eggs. >> >> >>> When I look at the logic being used here, especially at >>> https://bitbucket.org/galaxy/galaxy-central/src/f0ae870b22e9/lib/galaxy/eggs/?at=default >>> , it looks like a solution built exclusively for platforms on which pip is >>> not installed. >>> According to the wiki, Galaxy support only goes back as far as 2.6, and >>> get-pip.py supports 2.6, so there is no way of building a Galaxy server on >>> a platform that can't also have pip installed. >>> Adding pip to the requirements for Galaxy would not be particularly >>> onerous, and may simplify things significantly (no need to bundle >>> get-pip.py or similar). >>> >> >> As mentioned above, we don't use or depend on pip, so it's not required. >> That said, a lot of our egg fetching logic could likely be replaced with >> pip (this code predates pip by a few years). And the eggs could probably be >> replaced with prebuilt wheels. However, even if we did use pip/wheels, we'd >> need to install them from our own repository, and it'd still require >> modifications for binary platform incompatibilities. The egg handling code >> we have now works pretty reliably, so I am not sure there is a whole lot to >> be gained by changing it until Python finally figures out how to handle >> binary compatibility properly. >> >> >>> As a last note about the misleading error from the fetch_eggs script, >>> telling me that WebError is "NotFetchable". >>> I probably wouldn't have much of a complaint about this if the error had >>> been more on target and I hadn't felt the need to do things like patch >>> lib/galaxy/eggs to print a stacktrace. >>> For example, if the script detected that there was a source installed >>> package which was getting underfoot, it should have alerted me or even >>> suggested installing my various packages in egg format. >>> >> >> This is a bug - it is supposed to explain that there is a version >> conflict. If you have a stack trace, please send it along. >> >> >>> That kind of error detection is hard to maintain and hard to keep >>> accurate since the Galaxy team's priority is to build Galaxy, not a package >>> manager. >>> This, I suppose, circles back to an earlier question: why isn't Galaxy >>> using a python package manager to... manage its packages? >>> >>> >>> At the very least something along the lines of >>> `./scripts/common_setup.sh --use-pip` should be added. >>> It doesn't seem like it would be that hard to implement -- but I feel >>> like my lack of knowledge of Galaxy disqualifies me from building the >>> changeset reliably. >>> Of course, if no one objects, I will readily do so anyway (when I have >>> the time) as a proof of concept. >>> >> >> There are modifications to a few of the dependencies, such as psycopg2. >> When psycopg2 is scrambled, the scrambling process fetches and compiles a >> bit of PostgreSQL's libpq and then statically links to it to provide a >> standalone egg that does not depend on the user having installed libpq on >> their system. So a pip-based system that allowed building from source would >> need to account for this. >> >> --nate >> >> >>> Barring even that improvement, the Wiki page at >>> https://wiki.galaxyproject.org/Admin/Config/Eggs should definitely be >>> updated to include some note on why Galaxy has this complex logic for >>> fetching eggs instead of using pip. >>> >>> >>> A quick tl;dr and summary: >>> - I don't have extensive experience with Galaxy, so I may not know what >>> I'm talking about. >>> - fetch_eggs.py can be made to raise EggNotFetchable by doing a pip >>> install from a VCS without using `--egg`. This is a bug in fetch_eggs.py >>> - All supported platforms for Galaxy support pip >>> - Galaxy should have an option to use pip to download its packages over >>> https from eggs.g2.bx.psu.edu >>> - Galaxy should probably default to using pip when it's available, since >>> its failure modes are significantly better than a home-brewed package >>> manager -- this also leads to good behavior in virtualenvs. >>> >>> >>> Best regards, and many thanks for your time and attention, >>> -Stephen >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
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