single source for requirements

[prjemian]

As noted by @mrakitin, requirements.txt could/should be the single source for installation package requirements. At present, it is ignored.

Recommends placing all the deps to requirements.txt and read/parse this file in apstools/apstools/__init__.py, reducing this list to a single source.

[prjemian]

Add this in a fork from https://github.com/mrakitin/apstools/tree/fix-conda-recipe-and-pip-deps and contribute to the PR from @mrakitin. The fork is here.

[prjemian]

@mrakitin: Can you take a look at my fork? I'm still having a problem with the conda build ./conda-recipe/:

`conda build ./conda-recipe/` console log

No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
Copying /home/mintadmin/Documents/eclipse/apstools-prj to /home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/work
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Attempting to finalize metadata for apstools
INFO:conda_build.metadata:Attempting to finalize metadata for apstools
Collecting package metadata: ...working... done
Solving environment: ...working... done
Collecting package metadata: ...working... done
Solving environment: ...working... done
BUILD START: ['apstools-1.1.0+6.gf6aa515.dirty-py_0.tar.bz2']
Collecting package metadata: ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place


The following NEW packages will be INSTALLED:

    asn1crypto:          0.24.0-py37_0                           
    asteval:             0.9.12-py37h5ca1d4c_0   lightsource2-tag
    astropy:             3.1.2-py37h7b6447c_0                    
    atomicwrites:        1.3.0-py37_1                            
    attrs:               19.1.0-py37_1                           
    backcall:            0.1.0-py37_0                            
    blas:                1.0-mkl                                 
    bluesky:             1.5.2-py37_1            lightsource2-tag
    bokeh:               1.1.0-py37_0                            
    boltons:             16.3.1-py37_0           lightsource2-tag
    bottleneck:          1.2.1-py37h035aef0_1                    
    ca-certificates:     2019.1.23-0                             
    certifi:             2019.3.9-py37_0                         
    cffi:                1.12.3-py37h2e261b9_0                   
    chardet:             3.0.4-py37_1                            
    click:               7.0-py37_0                              
    cloudpickle:         0.8.1-py_0                              
    cryptography:        2.6.1-py37h1ba5d50_0                    
    cycler:              0.10.0-py37_0                           
    cytoolz:             0.9.0.1-py37h14c3975_1                  
    dask:                1.2.0-py_0                              
    dask-core:           1.2.0-py_0                              
    databroker:          0.12.2-py37_0           lightsource2-tag
    dbus:                1.13.6-h746ee38_0                       
    decorator:           4.4.0-py37_1                            
    dill:                0.2.9-py37_0                            
    distributed:         1.27.1-py37_0                           
    doct:                1.0.5-py37_0            lightsource2-tag
    epics-base:          3.14.12.6-3             lightsource2-tag
    event-model:         1.9.0-py37_0            lightsource2-tag
    expat:               2.2.6-he6710b0_0                        
    fast-histogram:      0.7-py37hdd07704_1000                   
    fontconfig:          2.13.0-h9420a91_0                       
    freetype:            2.9.1-h8a8886c_1                        
    glib:                2.56.2-hd408876_0                       
    glue-core:           0.14.2-py37_0                           
    glue-vispy-viewers:  0.11-py_0                               
    glueviz:             0.13.3-0                                
    gst-plugins-base:    1.14.0-hbbd80ab_1                       
    gstreamer:           1.14.0-hb453b48_1                       
    h5py:                2.9.0-py37h7918eee_0                    
    hdf5:                1.10.4-hb1b8bf9_0                       
    heapdict:            1.0.0-py37_2                            
    historydict:         1.2.3-py_0              lightsource2-tag
    humanize:            0.5.1-py37_1                            
    icu:                 58.2-h9c2bf20_1                         
    idna:                2.8-py37_0                              
    imageio:             2.5.0-py37_0                            
    intel-openmp:        2019.3-199                              
    ipykernel:           5.1.0-py37h39e3cac_0                    
    ipython:             7.5.0-py37h39e3cac_0                    
    ipython_genutils:    0.2.0-py37_0                            
    jedi:                0.13.3-py37_0                           
    jinja2:              2.10.1-py37_0                           
    jpeg:                9b-h024ee3a_2                           
    jsonschema:          2.6.0-py37_0                            
    jupyter_client:      5.2.4-py37_0                            
    jupyter_core:        4.4.0-py37_0                            
    kiwisolver:          1.1.0-py37he6710b0_0                    
    libedit:             3.1.20181209-hc058e9b_0                 
    libffi:              3.2.1-hd88cf55_4                        
    libgcc-ng:           8.2.0-hdf63c60_1                        
    libgfortran-ng:      7.3.0-hdf63c60_0                        
    libpng:              1.6.37-hbc83047_0                       
    libsodium:           1.0.16-h1bed415_0                       
    libstdcxx-ng:        8.2.0-hdf63c60_1                        
    libtiff:             4.0.10-h2733197_2                       
    libuuid:             1.0.3-h1bed415_2                        
    libxcb:              1.13-h1bed415_1                         
    libxml2:             2.9.9-he19cac6_0                        
    lmfit:               0.9.9-pyh5ca1d4c_0      lightsource2-tag
    locket:              0.2.0-py37_1                            
    markupsafe:          1.1.1-py37h7b6447c_0                    
    matplotlib:          3.0.3-py37h5429711_0                    
    mkl:                 2019.3-199                              
    mkl_fft:             1.0.12-py37ha843d7b_0                   
    mkl_random:          1.0.2-py37hd81dba3_0                    
    mongoquery:          1.1.0-py37_0            lightsource2-tag
    more-itertools:      7.0.0-py37_0                            
    mpl-scatter-density: 0.5-py_0                                
    msgpack-python:      0.6.1-py37hfd86e86_1                    
    nbformat:            4.4.0-py37_0                            
    ncurses:             6.1-he6710b0_1                          
    networkx:            2.3-py_0                                
    numpy:               1.16.3-py37h7e9f1db_0                   
    numpy-base:          1.16.3-py37hde5b4d6_0                   
    olefile:             0.46-py37_0                             
    openssl:             1.1.1b-h7b6447c_1                       
    ophyd:               1.3.3-py37_0            lightsource2-tag
    packaging:           19.0-py37_0                             
    pandas:              0.24.2-py37he6710b0_0                   
    parso:               0.4.0-py_0                              
    partd:               0.3.10-py37_1                           
    pcre:                8.43-he6710b0_0                         
    pexpect:             4.7.0-py37_0                            
    pickleshare:         0.7.5-py37_0                            
    pillow:              6.0.0-py37h34e0f95_0                    
    pims:                0.4.1-py_1              lightsource2-tag
    pip:                 19.1-py37_0                             
    plotly:              3.8.1-py_0                              
    pluggy:              0.9.0-py37_0                            
    prettytable:         0.7.2-py37_0            lightsource2-tag
    prompt_toolkit:      2.0.9-py37_0                            
    psutil:              5.6.2-py37h7b6447c_0                    
    ptyprocess:          0.6.0-py37_0                            
    py:                  1.8.0-py37_0                            
    pycparser:           2.19-py37_0                             
    pyepics:             3.3.0-py37h5ca1d4c_1    lightsource2-tag
    pygments:            2.3.1-py37_0                            
    pymongo:             3.7.2-py37he6710b0_0                    
    pyopengl:            3.1.1a1-py37_0                          
    pyopenssl:           19.0.0-py37_0                           
    pyparsing:           2.4.0-py_0                              
    pyqt:                5.9.2-py37h05f1152_2                    
    pyresttable:         2019.0321.0-py_0        local           
    pysocks:             1.6.8-py37_0                            
    pytest:              4.4.1-py37_0                            
    pytest-arraydiff:    0.3-py37h39e3cac_0                      
    pytest-astropy:      0.5.0-py37_0                            
    pytest-doctestplus:  0.3.0-py37_0                            
    pytest-openfiles:    0.3.2-py37_0                            
    pytest-remotedata:   0.3.1-py37_0                            
    python:              3.7.3-h0371630_0                        
    python-dateutil:     2.8.0-py37_0                            
    pytz:                2019.1-py_0                             
    pywavelets:          1.0.3-py37hdd07704_1                    
    pyyaml:              5.1-py37h7b6447c_0                      
    pyzmq:               18.0.0-py37he6710b0_0                   
    qt:                  5.9.7-h5867ecd_1                        
    qtconsole:           4.4.3-py37_0                            
    qtpy:                1.7.0-py37_1                            
    readline:            7.0-h7b6447c_5                          
    requests:            2.21.0-py37_0                           
    retrying:            1.3.3-py37_2                            
    scikit-image:        0.15.0-py37he6710b0_0                   
    scipy:               1.2.1-py37h7c811a0_0                    
    setuptools:          41.0.1-py37_0                           
    sip:                 4.19.8-py37hf484d3e_0                   
    six:                 1.12.0-py37_0                           
    slicerator:          0.9.8-py37h5ca1d4c_0    lightsource2-tag
    sortedcontainers:    2.1.0-py37_0                            
    sqlite:              3.28.0-h7b6447c_0                       
    super_state_machine: 1.0-py37_0              lightsource2-tag
    tblib:               1.3.2-py37_0                            
    tifffile:            0.11.1-py37_1           lightsource2-tag
    tk:                  8.6.8-hbc83047_0                        
    toolz:               0.9.0-py37_0                            
    tornado:             6.0.2-py37h7b6447c_0                    
    tqdm:                4.31.1-py37_1                           
    traitlets:           4.3.2-py37_0                            
    tzlocal:             1.5.1-py37_0                            
    ujson:               1.35-py37h14c3975_0                     
    urllib3:             1.24.2-py37_0                           
    wcwidth:             0.1.7-py37_0                            
    wheel:               0.33.1-py37_0                           
    xlrd:                1.2.0-py37_0                            
    xz:                  5.2.4-h14c3975_4                        
    yaml:                0.1.7-had09818_2                        
    zeromq:              4.3.1-he6710b0_3                        
    zict:                0.1.4-py37_0                            
    zlib:                1.2.11-h7b6447c_3                       
    zstd:                1.3.7-h0b5b093_0                        

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata: ...working... done
Solving environment: ...working... done
Traceback (most recent call last):
  File "setup.py", line 43, in <module>
    python_requires  = package.__python_version_required__,
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/setuptools/__init__.py", line 145, in setup
    return distutils.core.setup(**attrs)
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/setuptools/command/install.py", line 67, in run
    self.do_egg_install()
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/setuptools/command/install.py", line 117, in do_egg_install
    cmd.run()
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/setuptools/command/easy_install.py", line 418, in run
    self.easy_install(spec, not self.no_deps)
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/setuptools/command/easy_install.py", line 660, in easy_install
    return self.install_item(None, spec, tmpdir, deps, True)
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/setuptools/command/easy_install.py", line 707, in install_item
    self.process_distribution(spec, dist, deps)
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/setuptools/command/easy_install.py", line 752, in process_distribution
    [requirement], self.local_index, self.easy_install
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/pkg_resources/__init__.py", line 782, in resolve
    replace_conflicting=replace_conflicting
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1065, in best_match
    return self.obtain(req, installer)
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1077, in obtain
    return installer(requirement)
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/setuptools/command/easy_install.py", line 667, in easy_install
    not self.always_copy, self.local_index
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/setuptools/package_index.py", line 658, in fetch_distribution
    self.find_packages(requirement)
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/setuptools/package_index.py", line 491, in find_packages
    self.scan_url(self.index_url + requirement.unsafe_name + '/')
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/setuptools/package_index.py", line 831, in scan_url
    self.process_url(url, True)
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.7/site-packages/setuptools/package_index.py", line 326, in process_url
    "Be sure to add all dependencies in the meta.yaml  url=%s" % url)
RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://pypi.org/simple/historydict/
WARNING: symlink_conda() is deprecated.
WARNING: symlink_conda() is deprecated.
source tree in: /home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/work
export PREFIX=/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place
export BUILD_PREFIX=/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/_build_env
export SRC_DIR=/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/work
running install
running bdist_egg
running egg_info
writing apstools.egg-info/PKG-INFO
writing dependency_links to apstools.egg-info/dependency_links.txt
writing entry points to apstools.egg-info/entry_points.txt
writing requirements to apstools.egg-info/requires.txt
writing top-level names to apstools.egg-info/top_level.txt
reading manifest file 'apstools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'apstools.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
copying apstools/__init__.py -> build/lib/apstools
UPDATING build/lib/apstools/_version.py
set build/lib/apstools/_version.py to '1.1.0+6.gf6aa515.dirty'
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/__init__.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/_version.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/devices.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/examples.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/run_snapshot_gui.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/suspenders.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/utils.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/snapshot.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/signals.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/plans.py -> build/bdist.linux-x86_64/egg/apstools
creating build/bdist.linux-x86_64/egg/apstools/synApps_ophyd
copying build/lib/apstools/synApps_ophyd/__init__.py -> build/bdist.linux-x86_64/egg/apstools/synApps_ophyd
copying build/lib/apstools/synApps_ophyd/busy.py -> build/bdist.linux-x86_64/egg/apstools/synApps_ophyd
copying build/lib/apstools/synApps_ophyd/swait.py -> build/bdist.linux-x86_64/egg/apstools/synApps_ophyd
copying build/lib/apstools/synApps_ophyd/sscan.py -> build/bdist.linux-x86_64/egg/apstools/synApps_ophyd
copying build/lib/apstools/synApps_ophyd/save_data.py -> build/bdist.linux-x86_64/egg/apstools/synApps_ophyd
copying build/lib/apstools/filewriters.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/textreadonly.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/run_snapshot.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/callbacks.py -> build/bdist.linux-x86_64/egg/apstools
copying build/lib/apstools/_requirements.py -> build/bdist.linux-x86_64/egg/apstools
byte-compiling build/bdist.linux-x86_64/egg/apstools/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/_version.py to _version.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/devices.py to devices.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/examples.py to examples.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/run_snapshot_gui.py to run_snapshot_gui.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/suspenders.py to suspenders.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/utils.py to utils.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/snapshot.py to snapshot.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/signals.py to signals.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/plans.py to plans.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/synApps_ophyd/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/synApps_ophyd/busy.py to busy.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/synApps_ophyd/swait.py to swait.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/synApps_ophyd/sscan.py to sscan.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/synApps_ophyd/save_data.py to save_data.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/filewriters.py to filewriters.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/textreadonly.py to textreadonly.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/run_snapshot.py to run_snapshot.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/callbacks.py to callbacks.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/apstools/_requirements.py to _requirements.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying apstools.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying apstools.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying apstools.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying apstools.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying apstools.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying apstools.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying apstools.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/apstools-1.1.0+6.gf6aa515.dirty-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing apstools-1.1.0+6.gf6aa515.dirty-py3.7.egg
creating $PREFIX/lib/python3.7/site-packages/apstools-1.1.0+6.gf6aa515.dirty-py3.7.egg
Extracting apstools-1.1.0+6.gf6aa515.dirty-py3.7.egg to $PREFIX/lib/python3.7/site-packages
Adding apstools 1.1.0+6.gf6aa515.dirty to easy-install.pth file
Installing apstools_plan_catalog script to $PREFIX/bin
Installing bluesky_snapshot script to $PREFIX/bin
Installing bluesky_snapshot_viewer script to $PREFIX/bin

Installed $PREFIX/lib/python3.7/site-packages/apstools-1.1.0+6.gf6aa515.dirty-py3.7.egg
Processing dependencies for apstools==1.1.0+6.gf6aa515.dirty
Searching for historydict
Traceback (most recent call last):
  File "/home/mintadmin/Apps/anaconda/bin/conda-build", line 11, in <module>
    sys.exit(main())
  File "/home/mintadmin/Apps/anaconda/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 456, in main
    execute(sys.argv[1:])
  File "/home/mintadmin/Apps/anaconda/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 447, in execute
    verify=args.verify, variants=args.variants)
  File "/home/mintadmin/Apps/anaconda/lib/python3.7/site-packages/conda_build/api.py", line 208, in build
    notest=notest, need_source_download=need_source_download, variants=variants)
  File "/home/mintadmin/Apps/anaconda/lib/python3.7/site-packages/conda_build/build.py", line 2311, in build_tree
    notest=notest,
  File "/home/mintadmin/Apps/anaconda/lib/python3.7/site-packages/conda_build/build.py", line 1477, in build
    cwd=src_dir, stats=build_stats)
  File "/home/mintadmin/Apps/anaconda/lib/python3.7/site-packages/conda_build/utils.py", line 374, in check_call_env
    return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
  File "/home/mintadmin/Apps/anaconda/lib/python3.7/site-packages/conda_build/utils.py", line 354, in _func_defaulting_env_to_os_environ
    raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557252846110/work/conda_build.sh']' returned non-zero exit status 1.

[mrakitin]

I am still seeing one problem (covered by my PR #130):

  script: python setup.py install

Another question: how to reproduce it? Which channels are used (I assume lightsource2-tag and some other with the pyresttable package)?

[mrakitin]

I wasn't able to find the pyresttable to proceed with the build. Is it packaged with conda?

[prjemian]

-c prjemian

[mrakitin]

Oh, I think I realized what's wrong with the recipe besides the script part. Using databroker[all] is only supported for pip-packages, but not for the conda ones.

Also, the host part is a bit overloaded. What you need there is python and pip as it's ~similar to the build section, meaning you don't need all the dependencies used to run the code. Can we have a PR from your fork/branch please? This way reviewing the code will be much easier. I'll be happy to leave a few suggestions there.

[prjemian]

Yes. Also, here is the revision you mentioned:

---: script: python setup.py install
+++: script: python -m pip install --no-deps --ignore-installed .

[prjemian]

conda build now progresses (still slowly) past the point that errored above

[prjemian]

Now, the build fails on my new code to find the requirements. Need to add in MANIFEST.in

current build log details

No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
Copying /home/mintadmin/Documents/eclipse/apstools-prj to /home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/work
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Attempting to finalize metadata for apstools
INFO:conda_build.metadata:Attempting to finalize metadata for apstools
Collecting package metadata: ...working... done
Solving environment: ...working... done
Collecting package metadata: ...working... done
Solving environment: ...working... done
BUILD START: ['apstools-1.1.0+9.g0ac5ae0.dirty-py_0.tar.bz2']
Collecting package metadata: ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place


The following NEW packages will be INSTALLED:

    ca-certificates: 2019.1.23-0            
    certifi:         2019.3.9-py37_0        
    libedit:         3.1.20181209-hc058e9b_0
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       8.2.0-hdf63c60_1       
    libstdcxx-ng:    8.2.0-hdf63c60_1       
    ncurses:         6.1-he6710b0_1         
    openssl:         1.1.1b-h7b6447c_1      
    pip:             19.1-py37_0            
    python:          3.7.3-h0371630_0       
    readline:        7.0-h7b6447c_5         
    setuptools:      41.0.1-py37_0          
    sqlite:          3.28.0-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.33.1-py37_0          
    xz:              5.2.4-h14c3975_4       
    zlib:            1.2.11-h7b6447c_3      

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata: ...working... done
Solving environment: ...working... done
source tree in: /home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/work
export PREFIX=/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place
export BUILD_PREFIX=/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/_build_env
export SRC_DIR=/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/work
Processing $SRC_DIR
Building wheels for collected packages: apstools
  Building wheel for apstools (setup.py): started
  Building wheel for apstools (setup.py): finished with status 'done'
  Stored in directory: /tmp/pip-ephem-wheel-cache-4wa8avp0/wheels/d4/13/f0/e8f6441ecfaf9b8cc7b47765e41f71b4cd25f789dcf7b1ae75
Successfully built apstools
Installing collected packages: apstools
Successfully installed apstools-1.1.0+9.g0ac5ae0.dirty

Resource usage statistics from building apstools:
   Process count: 3
   CPU time: Sys=0:00:00.1, User=0:00:00.7
   Memory: 64.6M
   Disk usage: 3.5K
   Time elapsed: 0:00:04.1

Packaging apstools
WARNING: symlink_conda() is deprecated.
WARNING: symlink_conda() is deprecated.
INFO:conda_build.build:Packaging apstools
Packaging apstools-1.1.0+9.g0ac5ae0.dirty-py_0
INFO:conda_build.build:Packaging apstools-1.1.0+9.g0ac5ae0.dirty-py_0
nm: dynamic_annotations.o: no symbols
number of files: 30
Fixing permissions
Packaged license file.
Compressing to /tmp/tmpg9dyzw0t/apstools-1.1.0+9.g0ac5ae0.dirty-py_0.tar.bz2
Package verification results:
-----------------------------
TEST START: /home/mintadmin/Apps/anaconda/conda-bld/noarch/apstools-1.1.0+9.g0ac5ae0.dirty-py_0.tar.bz2
Adding in variants from /tmp/tmpslemo_2o/info/recipe/conda_build_config.yaml
/tmp/tmpg9dyzw0t/apstools-1.1.0+9.g0ac5ae0.dirty-py_0.tar.bz2: C1105 Found invalid version number in info/index.json
INFO:conda_build.variants:Adding in variants from /tmp/tmpslemo_2o/info/recipe/conda_build_config.yaml
Renaming work directory,  /home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/work  to  /home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/work_moved_apstools-1.1.0+9.g0ac5ae0.dirty-py_0_noarch
Collecting package metadata: ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl


The following NEW packages will be INSTALLED:

    apstools:            1.1.0+9.g0ac5ae0.dirty-py_0 local           
    asn1crypto:          0.24.0-py37_0                               
    asteval:             0.9.12-py37h5ca1d4c_0       lightsource2-tag
    astropy:             3.1.2-py37h7b6447c_0                        
    atomicwrites:        1.3.0-py37_1                                
    attrs:               19.1.0-py37_1                               
    backcall:            0.1.0-py37_0                                
    blas:                1.0-mkl                                     
    bluesky:             1.5.2-py37_1                lightsource2-tag
    bokeh:               1.1.0-py37_0                                
    boltons:             16.3.1-py37_0               lightsource2-tag
    bottleneck:          1.2.1-py37h035aef0_1                        
    ca-certificates:     2019.1.23-0                                 
    certifi:             2019.3.9-py37_0                             
    cffi:                1.12.3-py37h2e261b9_0                       
    chardet:             3.0.4-py37_1                                
    click:               7.0-py37_0                                  
    cloudpickle:         0.8.1-py_0                                  
    cryptography:        2.6.1-py37h1ba5d50_0                        
    cycler:              0.10.0-py37_0                               
    cytoolz:             0.9.0.1-py37h14c3975_1                      
    dask:                1.2.0-py_0                                  
    dask-core:           1.2.0-py_0                                  
    databroker:          0.12.2-py37_0               lightsource2-tag
    dbus:                1.13.6-h746ee38_0                           
    decorator:           4.4.0-py37_1                                
    dill:                0.2.9-py37_0                                
    distributed:         1.27.1-py37_0                               
    doct:                1.0.5-py37_0                lightsource2-tag
    epics-base:          3.14.12.6-3                 lightsource2-tag
    event-model:         1.9.0-py37_0                lightsource2-tag
    expat:               2.2.6-he6710b0_0                            
    fast-histogram:      0.7-py37hdd07704_1000                       
    fontconfig:          2.13.0-h9420a91_0                           
    freetype:            2.9.1-h8a8886c_1                            
    glib:                2.56.2-hd408876_0                           
    glue-core:           0.14.2-py37_0                               
    glue-vispy-viewers:  0.11-py_0                                   
    glueviz:             0.13.3-0                                    
    gst-plugins-base:    1.14.0-hbbd80ab_1                           
    gstreamer:           1.14.0-hb453b48_1                           
    h5py:                2.9.0-py37h7918eee_0                        
    hdf5:                1.10.4-hb1b8bf9_0                           
    heapdict:            1.0.0-py37_2                                
    historydict:         1.2.3-py_0                  lightsource2-tag
    humanize:            0.5.1-py37_1                                
    icu:                 58.2-h9c2bf20_1                             
    idna:                2.8-py37_0                                  
    imageio:             2.5.0-py37_0                                
    intel-openmp:        2019.3-199                                  
    ipykernel:           5.1.0-py37h39e3cac_0                        
    ipython:             7.5.0-py37h39e3cac_0                        
    ipython_genutils:    0.2.0-py37_0                                
    jedi:                0.13.3-py37_0                               
    jinja2:              2.10.1-py37_0                               
    jpeg:                9b-h024ee3a_2                               
    jsonschema:          2.6.0-py37_0                                
    jupyter_client:      5.2.4-py37_0                                
    jupyter_core:        4.4.0-py37_0                                
    kiwisolver:          1.1.0-py37he6710b0_0                        
    libedit:             3.1.20181209-hc058e9b_0                     
    libffi:              3.2.1-hd88cf55_4                            
    libgcc-ng:           8.2.0-hdf63c60_1                            
    libgfortran-ng:      7.3.0-hdf63c60_0                            
    libpng:              1.6.37-hbc83047_0                           
    libsodium:           1.0.16-h1bed415_0                           
    libstdcxx-ng:        8.2.0-hdf63c60_1                            
    libtiff:             4.0.10-h2733197_2                           
    libuuid:             1.0.3-h1bed415_2                            
    libxcb:              1.13-h1bed415_1                             
    libxml2:             2.9.9-he19cac6_0                            
    lmfit:               0.9.9-pyh5ca1d4c_0          lightsource2-tag
    locket:              0.2.0-py37_1                                
    markupsafe:          1.1.1-py37h7b6447c_0                        
    matplotlib:          3.0.3-py37h5429711_0                        
    mkl:                 2019.3-199                                  
    mkl_fft:             1.0.12-py37ha843d7b_0                       
    mkl_random:          1.0.2-py37hd81dba3_0                        
    mongoquery:          1.1.0-py37_0                lightsource2-tag
    more-itertools:      7.0.0-py37_0                                
    mpl-scatter-density: 0.5-py_0                                    
    msgpack-python:      0.6.1-py37hfd86e86_1                        
    nbformat:            4.4.0-py37_0                                
    ncurses:             6.1-he6710b0_1                              
    networkx:            2.3-py_0                                    
    numpy:               1.16.3-py37h7e9f1db_0                       
    numpy-base:          1.16.3-py37hde5b4d6_0                       
    olefile:             0.46-py37_0                                 
    openssl:             1.1.1b-h7b6447c_1                           
    ophyd:               1.3.3-py37_0                lightsource2-tag
    packaging:           19.0-py37_0                                 
    pandas:              0.24.2-py37he6710b0_0                       
    parso:               0.4.0-py_0                                  
    partd:               0.3.10-py37_1                               
    pcre:                8.43-he6710b0_0                             
    pexpect:             4.7.0-py37_0                                
    pickleshare:         0.7.5-py37_0                                
    pillow:              6.0.0-py37h34e0f95_0                        
    pims:                0.4.1-py_1                  lightsource2-tag
    pip:                 19.1-py37_0                                 
    plotly:              3.8.1-py_0                                  
    pluggy:              0.9.0-py37_0                                
    prettytable:         0.7.2-py37_0                lightsource2-tag
    prompt_toolkit:      2.0.9-py37_0                                
    psutil:              5.6.2-py37h7b6447c_0                        
    ptyprocess:          0.6.0-py37_0                                
    py:                  1.8.0-py37_0                                
    pycparser:           2.19-py37_0                                 
    pyepics:             3.3.0-py37h5ca1d4c_1        lightsource2-tag
    pygments:            2.3.1-py37_0                                
    pymongo:             3.7.2-py37he6710b0_0                        
    pyopengl:            3.1.1a1-py37_0                              
    pyopenssl:           19.0.0-py37_0                               
    pyparsing:           2.4.0-py_0                                  
    pyqt:                5.9.2-py37h05f1152_2                        
    pyresttable:         2019.0321.0-py_0            local           
    pysocks:             1.6.8-py37_0                                
    pytest:              4.4.1-py37_0                                
    pytest-arraydiff:    0.3-py37h39e3cac_0                          
    pytest-astropy:      0.5.0-py37_0                                
    pytest-doctestplus:  0.3.0-py37_0                                
    pytest-openfiles:    0.3.2-py37_0                                
    pytest-remotedata:   0.3.1-py37_0                                
    python:              3.7.3-h0371630_0                            
    python-dateutil:     2.8.0-py37_0                                
    pytz:                2019.1-py_0                                 
    pywavelets:          1.0.3-py37hdd07704_1                        
    pyyaml:              5.1-py37h7b6447c_0                          
    pyzmq:               18.0.0-py37he6710b0_0                       
    qt:                  5.9.7-h5867ecd_1                            
    qtconsole:           4.4.3-py37_0                                
    qtpy:                1.7.0-py37_1                                
    readline:            7.0-h7b6447c_5                              
    requests:            2.21.0-py37_0                               
    retrying:            1.3.3-py37_2                                
    scikit-image:        0.15.0-py37he6710b0_0                       
    scipy:               1.2.1-py37h7c811a0_0                        
    setuptools:          41.0.1-py37_0                               
    sip:                 4.19.8-py37hf484d3e_0                       
    six:                 1.12.0-py37_0                               
    slicerator:          0.9.8-py37h5ca1d4c_0        lightsource2-tag
    sortedcontainers:    2.1.0-py37_0                                
    sqlite:              3.28.0-h7b6447c_0                           
    super_state_machine: 1.0-py37_0                  lightsource2-tag
    tblib:               1.3.2-py37_0                                
    tifffile:            0.11.1-py37_1               lightsource2-tag
    tk:                  8.6.8-hbc83047_0                            
    toolz:               0.9.0-py37_0                                
    tornado:             6.0.2-py37h7b6447c_0                        
    tqdm:                4.31.1-py37_1                               
    traitlets:           4.3.2-py37_0                                
    tzlocal:             1.5.1-py37_0                                
    ujson:               1.35-py37h14c3975_0                         
    urllib3:             1.24.2-py37_0                               
    wcwidth:             0.1.7-py37_0                                
    wheel:               0.33.1-py37_0                               
    xlrd:                1.2.0-py37_0                                
    xz:                  5.2.4-h14c3975_4                            
    yaml:                0.1.7-had09818_2                            
    zeromq:              4.3.1-he6710b0_3                            
    zict:                0.1.4-py37_0                                
    zlib:                1.2.11-h7b6447c_3                           
    zstd:                1.3.7-h0b5b093_0                            

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Traceback (most recent call last):
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/test_tmp/run_test.py", line 2, in <module>
    import apstools
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.7/site-packages/apstools/__init__.py", line 30, in <module>
    __install_requires__ = learn_requirements()
  File "/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.7/site-packages/apstools/_requirements.py", line 28, in learn_requirements
    with open(req_file, 'r') as fp:
FileNotFoundError: [Errno 2] No such file or directory: '/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.7/site-packages/apstools/../requirements.txt'
WARNING: symlink_conda() is deprecated.
Tests failed for apstools-1.1.0+9.g0ac5ae0.dirty-py_0.tar.bz2 - moving package to /home/mintadmin/Apps/anaconda/conda-bld/broken
WARNING:conda_build.build:Tests failed for apstools-1.1.0+9.g0ac5ae0.dirty-py_0.tar.bz2 - moving package to /home/mintadmin/Apps/anaconda/conda-bld/broken
export PREFIX=/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl
export SRC_DIR=/home/mintadmin/Apps/anaconda/conda-bld/apstools_1557255019566/test_tmp
import: 'apstools'
TESTS FAILED: apstools-1.1.0+9.g0ac5ae0.dirty-py_0.tar.bz2

[mrakitin]

Ha, I posted the same in mrakitin#1 (comment).

[mrakitin]

I think the problem is that relative path to the sources, namely, it cannot find the specified requirements file in .../site-packages/apstools/../requirements.txt, which, I guess, should be .../site-packages/apstools/requirements.txt.