Date   
Bottleneck distances

Adam Spannaus
 

Hi Dimitri,

I am having an issue when computing the bottleneck distance between two diagrams. When both persistence diagrams have a point that has inf as its death time, the bottleneck distance seems to hang and not return a value. When computing these same values using the TDA package in R, I am able to compute these same distances, as it sets some finite number for the death at inf.  Also, since the death time is an attribute, I cannot change it in my code to be some large number.

Thanks for the assistance,
Adam

Re: Error Installing via pip on Cloud9/AWS (Ubuntu instance)

E. Noel Brown (SavageDuck) <enoelbrown@...>
 

Nevermind. I needed the full directory. Sorry, it's been awhile since I've touched Python.

Re: Error Installing via pip on Cloud9/AWS (Ubuntu instance)

E. Noel Brown (SavageDuck) <enoelbrown@...>
 

Okay, I discovered the problem was AWS doesn't automatically setup a swap partition. I created a 1GB swap and then pip seemed to successfully install dionysus.

I am now trying to get the following test python code to compile:
http://www.mrzv.org/software/dionysus/examples/alphashape.html#alpha-shape-example

Python successfully imports Filtration, but then cannot find any of the other names dionysus names to import.

Re: Error Installing via pip on Cloud9/AWS (Ubuntu instance)

Dmitriy Morozov
 

It's very unlikely that the compiler is frozen. It sounds like this is an issue with Cloud9, not Dionysus.

On Fri, Apr 20, 2018 at 9:40 AM, E. Noel Brown (SavageDuck) <enoelbrown@...> wrote:

Dmitriy:

Yes, I switched, and I apologize for the OS confusion. I decided to try an Ubuntu instance via Cloud9 instead of Cygwin for the time being.

I also spotted the error about Boost and added the environment variable. I then reran the pip command, and it is currently installing. I'm now sitting at 14% while the filtration compilation is happening. Below is my current progress, and it seems frozen at filtration once more. Last time, I allowed it to sit and compile for 15 minutes. It has been 9 minutes so far into this attempt.

Created temporary directory: /tmp/pip-ephem-wheel-cache-zjlXIE

Created temporary directory: /tmp/pip-install-12_Ygo

Collecting dionysus

  1 location(s) to search for versions of dionysus:

  * https://pypi.org/simple/dionysus/

  Getting page https://pypi.org/simple/dionysus/

  Looking up "https://pypi.org/simple/dionysus/" in the cache

  Current age based on date: 1452

  Freshness lifetime from max-age: 600

  Freshness lifetime from request max-age: 600

  Starting new HTTPS connection (1): pypi.org

  https://pypi.org:443 "GET /simple/dionysus/ HTTP/1.1" 304 0

  Analyzing links from page https://pypi.org/simple/dionysus/

    Found link https://files.pythonhosted.org/packages/cf/58/4f56cbc4125ae89f69b2862107014e06fc6a12a36b7fb6e94ad95eab36c3/dionysus-2.0.1.tar.gz#sha256=040e45d9bd415dfdc02dd9bf257affe9e865c029dbfef9d703144e6cf7311fcf (from https://pypi.org/simple/dionysus/), version: 2.0.1

    Found link https://files.pythonhosted.org/packages/47/5f/fdff2b2868de745a07614077f303bb45316644bc032ebfaca1436d728440/dionysus-2.0.2.tar.gz#sha256=78c24da06fd273f0103ad4cb86331f5f4518d7f0445e2cecd0e325ca1a2d011f (from https://pypi.org/simple/dionysus/), version: 2.0.2

    Found link https://files.pythonhosted.org/packages/20/77/e6395687eb442e7dcb37ceb3ad5646f222ac74739b0aa186189a22085ee7/dionysus-2.0.3.tar.gz#sha256=cdd44b3dfd7199290f28af1b6d3fdd61167db231601330a9b73cad083a86366d (from https://pypi.org/simple/dionysus/), version: 2.0.3

    Found link https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz#sha256=e411396c63aa6838e414c18979d4d90a28fcc60ae1660389e6b777a43479bf40 (from https://pypi.org/simple/dionysus/), version: 2.0.4

  Using version 2.0.4 (newest of versions: 2.0.1, 2.0.2, 2.0.3, 2.0.4)

  Created temporary directory: /tmp/pip-unpack-YCA57f

  Looking up "https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz" in the cache

  Ignoring unknown cache-control directive: 

  Current age based on date: 2127

  Ignoring unknown cache-control directive: immutable

  Freshness lifetime from max-age: 365000000

  The response is "fresh", returning cached response

  365000000 > 2127

  Using cached https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz

  Downloading from URL https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz#sha256=e411396c63aa6838e414c18979d4d90a28fcc60ae1660389e6b777a43479bf40 (from https://pypi.org/simple/dionysus/)

  Running setup.py (path:/tmp/pip-install-12_Ygo/dionysus/setup.py) egg_info for package dionysus

    Running command python setup.py egg_info

    running egg_info

    creating pip-egg-info/dionysus.egg-info

    writing pip-egg-info/dionysus.egg-info/PKG-INFO

    writing top-level names to pip-egg-info/dionysus.egg-info/top_level.txt

    writing dependency_links to pip-egg-info/dionysus.egg-info/dependency_links.txt

    writing manifest file 'pip-egg-info/dionysus.egg-info/SOURCES.txt'

    warning: manifest_maker: standard file '-c' not found

 

    reading manifest file 'pip-egg-info/dionysus.egg-info/SOURCES.txt'

    reading manifest template 'MANIFEST.in'

    warning: no files found matching '*' under directory '.'

    warning: no previously-included files matching '*' found under directory './.hg'

    warning: no previously-included files matching '*' found under directory './doc/_build'

    warning: no previously-included files matching '*' found under directory './dist'

    warning: no previously-included files found matching '.hgignore'

    warning: no previously-included files found matching '.hgsubtree'

    warning: no previously-included files found matching 'tags'

    warning: no previously-included files matching '*.orig' found under directory '.'

    writing manifest file 'pip-egg-info/dionysus.egg-info/SOURCES.txt'

  Source in /tmp/pip-install-12_Ygo/dionysus has version 2.0.4, which satisfies requirement dionysus from https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz#sha256=e411396c63aa6838e414c18979d4d90a28fcc60ae1660389e6b777a43479bf40

Building wheels for collected packages: dionysus

  Created temporary directory: /tmp/pip-wheel-Am8ZMP

  Running setup.py bdist_wheel for dionysus ...   Destination directory: /tmp/pip-wheel-Am8ZMP

  Running command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-12_Ygo/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-Am8ZMP --python-tag cp27

  running bdist_wheel

  running build

  running build_py

  creating build

  creating build/lib.linux-x86_64-2.7

  creating build/lib.linux-x86_64-2.7/dionysus

  copying bindings/python/dionysus/_version.py -> build/lib.linux-x86_64-2.7/dionysus

  copying bindings/python/dionysus/__init__.py -> build/lib.linux-x86_64-2.7/dionysus

  copying bindings/python/dionysus/plot.py -> build/lib.linux-x86_64-2.7/dionysus

  running build_ext

  -- The C compiler identification is GNU 5.4.0

  -- The CXX compiler identification is GNU 5.4.0

  -- Check for working C compiler: /usr/bin/cc

  -- Check for working C compiler: /usr/bin/cc -- works

  -- Detecting C compiler ABI info

  -- Detecting C compiler ABI info - done

  -- Detecting C compile features

  -- Detecting C compile features - done

  -- Check for working CXX compiler: /usr/bin/c++

  -- Check for working CXX compiler: /usr/bin/c++ -- works

  -- Detecting CXX compiler ABI info

  -- Detecting CXX compiler ABI info - done

  -- Detecting CXX compile features

  -- Detecting CXX compile features - done

  -- Boost version: 1.67.0

  -- Found PythonInterp: /usr/bin/python (found version "2.7.12")

  -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so

  -- Performing Test HAS_CPP14_FLAG

  -- Performing Test HAS_CPP14_FLAG - Success

  -- pybind11 v2.2.0

  -- Performing Test HAS_FLTO

  -- Performing Test HAS_FLTO - Success

  -- LTO enabled

  -- Configuring done

  -- Generating done

  -- Build files have been written to: /tmp/pip-install-12_Ygo/dionysus/build/temp.linux-x86_64-2.7

  Scanning dependencies of target dionysus

  [  0%] Built target dionysus

  Scanning dependencies of target _dionysus

  [  7%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dionysus.cpp.o

 

  [ 14%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/filtration.cpp.o


Re: Error Installing via pip on Cloud9/AWS (Ubuntu instance)

E. Noel Brown (SavageDuck) <enoelbrown@...>
 

Dmitriy:

Yes, I switched, and I apologize for the OS confusion. I decided to try an Ubuntu instance via Cloud9 instead of Cygwin for the time being.

I also spotted the error about Boost and added the environment variable. I then reran the pip command, and it is currently installing. I'm now sitting at 14% while the filtration compilation is happening. Below is my current progress, and it seems frozen at filtration once more. Last time, I allowed it to sit and compile for 15 minutes. It has been 9 minutes so far into this attempt.

Created temporary directory: /tmp/pip-ephem-wheel-cache-zjlXIE

Created temporary directory: /tmp/pip-install-12_Ygo

Collecting dionysus

  1 location(s) to search for versions of dionysus:

  * https://pypi.org/simple/dionysus/

  Getting page https://pypi.org/simple/dionysus/

  Looking up "https://pypi.org/simple/dionysus/" in the cache

  Current age based on date: 1452

  Freshness lifetime from max-age: 600

  Freshness lifetime from request max-age: 600

  Starting new HTTPS connection (1): pypi.org

  https://pypi.org:443 "GET /simple/dionysus/ HTTP/1.1" 304 0

  Analyzing links from page https://pypi.org/simple/dionysus/

    Found link https://files.pythonhosted.org/packages/cf/58/4f56cbc4125ae89f69b2862107014e06fc6a12a36b7fb6e94ad95eab36c3/dionysus-2.0.1.tar.gz#sha256=040e45d9bd415dfdc02dd9bf257affe9e865c029dbfef9d703144e6cf7311fcf (from https://pypi.org/simple/dionysus/), version: 2.0.1

    Found link https://files.pythonhosted.org/packages/47/5f/fdff2b2868de745a07614077f303bb45316644bc032ebfaca1436d728440/dionysus-2.0.2.tar.gz#sha256=78c24da06fd273f0103ad4cb86331f5f4518d7f0445e2cecd0e325ca1a2d011f (from https://pypi.org/simple/dionysus/), version: 2.0.2

    Found link https://files.pythonhosted.org/packages/20/77/e6395687eb442e7dcb37ceb3ad5646f222ac74739b0aa186189a22085ee7/dionysus-2.0.3.tar.gz#sha256=cdd44b3dfd7199290f28af1b6d3fdd61167db231601330a9b73cad083a86366d (from https://pypi.org/simple/dionysus/), version: 2.0.3

    Found link https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz#sha256=e411396c63aa6838e414c18979d4d90a28fcc60ae1660389e6b777a43479bf40 (from https://pypi.org/simple/dionysus/), version: 2.0.4

  Using version 2.0.4 (newest of versions: 2.0.1, 2.0.2, 2.0.3, 2.0.4)

  Created temporary directory: /tmp/pip-unpack-YCA57f

  Looking up "https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz" in the cache

  Ignoring unknown cache-control directive: 

  Current age based on date: 2127

  Ignoring unknown cache-control directive: immutable

  Freshness lifetime from max-age: 365000000

  The response is "fresh", returning cached response

  365000000 > 2127

  Using cached https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz

  Downloading from URL https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz#sha256=e411396c63aa6838e414c18979d4d90a28fcc60ae1660389e6b777a43479bf40 (from https://pypi.org/simple/dionysus/)

  Running setup.py (path:/tmp/pip-install-12_Ygo/dionysus/setup.py) egg_info for package dionysus

    Running command python setup.py egg_info

    running egg_info

    creating pip-egg-info/dionysus.egg-info

    writing pip-egg-info/dionysus.egg-info/PKG-INFO

    writing top-level names to pip-egg-info/dionysus.egg-info/top_level.txt

    writing dependency_links to pip-egg-info/dionysus.egg-info/dependency_links.txt

    writing manifest file 'pip-egg-info/dionysus.egg-info/SOURCES.txt'

    warning: manifest_maker: standard file '-c' not found

 

    reading manifest file 'pip-egg-info/dionysus.egg-info/SOURCES.txt'

    reading manifest template 'MANIFEST.in'

    warning: no files found matching '*' under directory '.'

    warning: no previously-included files matching '*' found under directory './.hg'

    warning: no previously-included files matching '*' found under directory './doc/_build'

    warning: no previously-included files matching '*' found under directory './dist'

    warning: no previously-included files found matching '.hgignore'

    warning: no previously-included files found matching '.hgsubtree'

    warning: no previously-included files found matching 'tags'

    warning: no previously-included files matching '*.orig' found under directory '.'

    writing manifest file 'pip-egg-info/dionysus.egg-info/SOURCES.txt'

  Source in /tmp/pip-install-12_Ygo/dionysus has version 2.0.4, which satisfies requirement dionysus from https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz#sha256=e411396c63aa6838e414c18979d4d90a28fcc60ae1660389e6b777a43479bf40

Building wheels for collected packages: dionysus

  Created temporary directory: /tmp/pip-wheel-Am8ZMP

  Running setup.py bdist_wheel for dionysus ...   Destination directory: /tmp/pip-wheel-Am8ZMP

  Running command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-12_Ygo/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-Am8ZMP --python-tag cp27

  running bdist_wheel

  running build

  running build_py

  creating build

  creating build/lib.linux-x86_64-2.7

  creating build/lib.linux-x86_64-2.7/dionysus

  copying bindings/python/dionysus/_version.py -> build/lib.linux-x86_64-2.7/dionysus

  copying bindings/python/dionysus/__init__.py -> build/lib.linux-x86_64-2.7/dionysus

  copying bindings/python/dionysus/plot.py -> build/lib.linux-x86_64-2.7/dionysus

  running build_ext

  -- The C compiler identification is GNU 5.4.0

  -- The CXX compiler identification is GNU 5.4.0

  -- Check for working C compiler: /usr/bin/cc

  -- Check for working C compiler: /usr/bin/cc -- works

  -- Detecting C compiler ABI info

  -- Detecting C compiler ABI info - done

  -- Detecting C compile features

  -- Detecting C compile features - done

  -- Check for working CXX compiler: /usr/bin/c++

  -- Check for working CXX compiler: /usr/bin/c++ -- works

  -- Detecting CXX compiler ABI info

  -- Detecting CXX compiler ABI info - done

  -- Detecting CXX compile features

  -- Detecting CXX compile features - done

  -- Boost version: 1.67.0

  -- Found PythonInterp: /usr/bin/python (found version "2.7.12")

  -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so

  -- Performing Test HAS_CPP14_FLAG

  -- Performing Test HAS_CPP14_FLAG - Success

  -- pybind11 v2.2.0

  -- Performing Test HAS_FLTO

  -- Performing Test HAS_FLTO - Success

  -- LTO enabled

  -- Configuring done

  -- Generating done

  -- Build files have been written to: /tmp/pip-install-12_Ygo/dionysus/build/temp.linux-x86_64-2.7

  Scanning dependencies of target dionysus

  [  0%] Built target dionysus

  Scanning dependencies of target _dionysus

  [  7%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dionysus.cpp.o

 

  [ 14%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/filtration.cpp.o

Re: Error Installing via pip on Cloud9/AWS (Ubuntu instance)

Dmitriy Morozov
 

This is not the Cygwin issue you brought up on GitHub. This particular problem is simply you needing to install Boost on your Ubuntu box. Something like "apt-get install boost" should work, I think, but I'm not a Ubuntu user.

On Fri, Apr 20, 2018 at 9:27 AM, E. Noel Brown (SavageDuck) <emma.n.brown@...> wrote:
Hello all. I'm terribly new to a lot of stuff involved here. I'm trying to help a friend get Dionysus up and running using Cloud9 IDE through AWS (Ubuntu instance).

I have Python 2.7 installed and tried to go the route of installing Dionysus 2 using pip. First time through, it seemed to be installing, but then my terminal froze when it started compiling the included filtration example. When I tried to rerun pip, this is the error I received. I'm not sure where to go from here and would appreciate any help.

Created temporary directory: /tmp/pip-ephem-wheel-cache-I4caxr
Created temporary directory: /tmp/pip-install-IsduFR
Collecting dionysus
  1 location(s) to search for versions of dionysus:
  Looking up "https://pypi.org/simple/dionysus/" in the cache
  Current age based on date: 536
  Freshness lifetime from max-age: 600
  Freshness lifetime from request max-age: 600
  The response is "fresh", returning cached response
  600 > 536
  Analyzing links from page https://pypi.org/simple/dionysus/
  Using version 2.0.4 (newest of versions: 2.0.1, 2.0.2, 2.0.3, 2.0.4)
  Created temporary directory: /tmp/pip-unpack-yLZ8qk
  Ignoring unknown cache-control directive: 
  Current age based on date: 1210
  Ignoring unknown cache-control directive: immutable
  Freshness lifetime from max-age: 365000000
  The response is "fresh", returning cached response
  365000000 > 1210
  Running setup.py (path:/tmp/pip-install-IsduFR/dionysus/setup.py) egg_info for package dionysus
    Running command python setup.py egg_info
    running egg_info
    creating pip-egg-info/dionysus.egg-info
    writing pip-egg-info/dionysus.egg-info/PKG-INFO
    writing top-level names to pip-egg-info/dionysus.egg-info/top_level.txt
    writing dependency_links to pip-egg-info/dionysus.egg-info/dependency_links.txt
    writing manifest file 'pip-egg-info/dionysus.egg-info/SOURCES.txt'
    warning: manifest_maker: standard file '-c' not found
 
    reading manifest file 'pip-egg-info/dionysus.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no files found matching '*' under directory '.'
    warning: no previously-included files matching '*' found under directory './.hg'
    warning: no previously-included files matching '*' found under directory './doc/_build'
    warning: no previously-included files matching '*' found under directory './dist'
    warning: no previously-included files found matching '.hgignore'
    warning: no previously-included files found matching '.hgsubtree'
    warning: no previously-included files found matching 'tags'
    warning: no previously-included files matching '*.orig' found under directory '.'
    writing manifest file 'pip-egg-info/dionysus.egg-info/SOURCES.txt'
Building wheels for collected packages: dionysus
  Created temporary directory: /tmp/pip-wheel-I26XHU
  Running setup.py bdist_wheel for dionysus ...   Destination directory: /tmp/pip-wheel-I26XHU
  Running command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-IsduFR/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-I26XHU --python-tag cp27
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-2.7
  creating build/lib.linux-x86_64-2.7/dionysus
  copying bindings/python/dionysus/_version.py -> build/lib.linux-x86_64-2.7/dionysus
  copying bindings/python/dionysus/__init__.py -> build/lib.linux-x86_64-2.7/dionysus
  copying bindings/python/dionysus/plot.py -> build/lib.linux-x86_64-2.7/dionysus
  running build_ext
  -- The C compiler identification is GNU 5.4.0
  -- The CXX compiler identification is GNU 5.4.0
  -- Check for working C compiler: /usr/bin/cc
  -- Check for working C compiler: /usr/bin/cc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- Check for working CXX compiler: /usr/bin/c++
  -- Check for working CXX compiler: /usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- Could NOT find Boost
  -- Found PythonInterp: /usr/bin/python (found version "2.7.12")
  -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so
  -- Performing Test HAS_CPP14_FLAG
  -- Performing Test HAS_CPP14_FLAG - Success
  -- pybind11 v2.2.0
  -- Performing Test HAS_FLTO
  -- Performing Test HAS_FLTO - Success
  -- LTO enabled
  CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
  Please set them or make sure they are set and tested correctly in the CMake files:
  Boost_INCLUDE_DIR (ADVANCED)
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python/pybind11
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python/pybind11
 
  -- Configuring incomplete, errors occurred!
  See also "/tmp/pip-install-IsduFR/dionysus/build/temp.linux-x86_64-2.7/CMakeFiles/CMakeOutput.log".
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/tmp/pip-install-IsduFR/dionysus/setup.py", line 97, in <module>
      zip_safe=False,
    File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
      dist.run_commands()
    File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
      self.run_command(cmd)
    File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/usr/lib/python2.7/dist-packages/wheel/bdist_wheel.py", line 179, in run
      self.run_command('build')
    File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
      self.distribution.run_command(command)
    File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/usr/lib/python2.7/distutils/command/build.py", line 128, in run
      self.run_command(cmd_name)
    File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
      self.distribution.run_command(command)
    File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/tmp/pip-install-IsduFR/dionysus/setup.py", line 39, in run
      self.build_extension(ext)
    File "/tmp/pip-install-IsduFR/dionysus/setup.py", line 64, in build_extension
      subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
    File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-IsduFR/dionysus', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-IsduFR/dionysus/build/lib.linux-x86_64-2.7', '-DPYTHON_EXECUTABLE=/usr/bin/python', '-Dbuild_examples=OFF', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1
error
  Failed building wheel for dionysus
  Running setup.py clean for dionysus
  Running command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-IsduFR/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" clean --all
  running clean
  removing 'build/temp.linux-x86_64-2.7' (and everything under it)
  removing 'build/lib.linux-x86_64-2.7' (and everything under it)
  'build/bdist.linux-x86_64' does not exist -- can't clean it
  'build/scripts-2.7' does not exist -- can't clean it
  removing 'build'
Failed to build dionysus
Installing collected packages: dionysus
  Created temporary directory: /tmp/pip-record-jmS7H0
  Running setup.py install for dionysus ...     Running command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-IsduFR/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-jmS7H0/install-record.txt --single-version-externally-managed --compile
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-2.7
    creating build/lib.linux-x86_64-2.7/dionysus
    copying bindings/python/dionysus/_version.py -> build/lib.linux-x86_64-2.7/dionysus
    copying bindings/python/dionysus/__init__.py -> build/lib.linux-x86_64-2.7/dionysus
    copying bindings/python/dionysus/plot.py -> build/lib.linux-x86_64-2.7/dionysus
    running build_ext
    -- The C compiler identification is GNU 5.4.0
    -- The CXX compiler identification is GNU 5.4.0
    -- Check for working C compiler: /usr/bin/cc
    -- Check for working C compiler: /usr/bin/cc -- works
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Detecting C compile features
    -- Detecting C compile features - done
    -- Check for working CXX compiler: /usr/bin/c++
    -- Check for working CXX compiler: /usr/bin/c++ -- works
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- Detecting CXX compile features
    -- Detecting CXX compile features - done
    -- Could NOT find Boost
    -- Found PythonInterp: /usr/bin/python (found version "2.7.12")
    -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so
    -- Performing Test HAS_CPP14_FLAG
    -- Performing Test HAS_CPP14_FLAG - Success
    -- pybind11 v2.2.0
    -- Performing Test HAS_FLTO
    -- Performing Test HAS_FLTO - Success
    -- LTO enabled
    CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
    Please set them or make sure they are set and tested correctly in the CMake files:
    Boost_INCLUDE_DIR (ADVANCED)
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python/pybind11
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python/pybind11
 
    -- Configuring incomplete, errors occurred!
    See also "/tmp/pip-install-IsduFR/dionysus/build/temp.linux-x86_64-2.7/CMakeFiles/CMakeOutput.log".
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-IsduFR/dionysus/setup.py", line 97, in <module>
        zip_safe=False,
      File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
        dist.run_commands()
      File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/usr/lib/python2.7/dist-packages/setuptools/command/install.py", line 61, in run
        return orig.install.run(self)
      File "/usr/lib/python2.7/distutils/command/install.py", line 601, in run
        self.run_command('build')
      File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
        self.distribution.run_command(command)
      File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/usr/lib/python2.7/distutils/command/build.py", line 128, in run
        self.run_command(cmd_name)
      File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
        self.distribution.run_command(command)
      File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/tmp/pip-install-IsduFR/dionysus/setup.py", line 39, in run
        self.build_extension(ext)
      File "/tmp/pip-install-IsduFR/dionysus/setup.py", line 64, in build_extension
        subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
      File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-IsduFR/dionysus', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-IsduFR/dionysus/build/lib.linux-x86_64-2.7', '-DPYTHON_EXECUTABLE=/usr/bin/python', '-Dbuild_examples=OFF', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1
error
Cleaning up...
  Removing source in /tmp/pip-install-IsduFR/dionysus
Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-IsduFR/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-jmS7H0/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-IsduFR/dionysus/
Exception information:
Traceback (most recent call last):
  File "/home/ubuntu/.local/lib/python2.7/site-packages/pip/_internal/basecommand.py", line 228, in main
    status = self.run(options, args)
  File "/home/ubuntu/.local/lib/python2.7/site-packages/pip/_internal/commands/install.py", line 335, in run
    use_user_site=options.use_user_site,
  File "/home/ubuntu/.local/lib/python2.7/site-packages/pip/_internal/req/__init__.py", line 49, in install_given_reqs
    **kwargs
  File "/home/ubuntu/.local/lib/python2.7/site-packages/pip/_internal/req/req_install.py", line 779, in install
    spinner=spinner,
  File "/home/ubuntu/.local/lib/python2.7/site-packages/pip/_internal/utils/misc.py", line 698, in call_subprocess
    % (command_desc, proc.returncode, cwd))
InstallationError: Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-IsduFR/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-jmS7H0/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-IsduFR/dionysus/


Error Installing via pip on Cloud9/AWS (Ubuntu instance)

E. Noel Brown (SavageDuck) <emma.n.brown@...>
 

Hello all. I'm terribly new to a lot of stuff involved here. I'm trying to help a friend get Dionysus up and running using Cloud9 IDE through AWS (Ubuntu instance).

I have Python 2.7 installed and tried to go the route of installing Dionysus 2 using pip. First time through, it seemed to be installing, but then my terminal froze when it started compiling the included filtration example. When I tried to rerun pip, this is the error I received. I'm not sure where to go from here and would appreciate any help.

Created temporary directory: /tmp/pip-ephem-wheel-cache-I4caxr
Created temporary directory: /tmp/pip-install-IsduFR
Collecting dionysus
  1 location(s) to search for versions of dionysus:
  * https://pypi.org/simple/dionysus/
  Getting page https://pypi.org/simple/dionysus/
  Looking up "https://pypi.org/simple/dionysus/" in the cache
  Current age based on date: 536
  Freshness lifetime from max-age: 600
  Freshness lifetime from request max-age: 600
  The response is "fresh", returning cached response
  600 > 536
  Analyzing links from page https://pypi.org/simple/dionysus/
    Found link https://files.pythonhosted.org/packages/cf/58/4f56cbc4125ae89f69b2862107014e06fc6a12a36b7fb6e94ad95eab36c3/dionysus-2.0.1.tar.gz#sha256=040e45d9bd415dfdc02dd9bf257affe9e865c029dbfef9d703144e6cf7311fcf (from https://pypi.org/simple/dionysus/), version: 2.0.1
    Found link https://files.pythonhosted.org/packages/47/5f/fdff2b2868de745a07614077f303bb45316644bc032ebfaca1436d728440/dionysus-2.0.2.tar.gz#sha256=78c24da06fd273f0103ad4cb86331f5f4518d7f0445e2cecd0e325ca1a2d011f (from https://pypi.org/simple/dionysus/), version: 2.0.2
    Found link https://files.pythonhosted.org/packages/20/77/e6395687eb442e7dcb37ceb3ad5646f222ac74739b0aa186189a22085ee7/dionysus-2.0.3.tar.gz#sha256=cdd44b3dfd7199290f28af1b6d3fdd61167db231601330a9b73cad083a86366d (from https://pypi.org/simple/dionysus/), version: 2.0.3
    Found link https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz#sha256=e411396c63aa6838e414c18979d4d90a28fcc60ae1660389e6b777a43479bf40 (from https://pypi.org/simple/dionysus/), version: 2.0.4
  Using version 2.0.4 (newest of versions: 2.0.1, 2.0.2, 2.0.3, 2.0.4)
  Created temporary directory: /tmp/pip-unpack-yLZ8qk
  Looking up "https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz" in the cache
  Ignoring unknown cache-control directive: 
  Current age based on date: 1210
  Ignoring unknown cache-control directive: immutable
  Freshness lifetime from max-age: 365000000
  The response is "fresh", returning cached response
  365000000 > 1210
  Using cached https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz
  Downloading from URL https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz#sha256=e411396c63aa6838e414c18979d4d90a28fcc60ae1660389e6b777a43479bf40 (from https://pypi.org/simple/dionysus/)
  Running setup.py (path:/tmp/pip-install-IsduFR/dionysus/setup.py) egg_info for package dionysus
    Running command python setup.py egg_info
    running egg_info
    creating pip-egg-info/dionysus.egg-info
    writing pip-egg-info/dionysus.egg-info/PKG-INFO
    writing top-level names to pip-egg-info/dionysus.egg-info/top_level.txt
    writing dependency_links to pip-egg-info/dionysus.egg-info/dependency_links.txt
    writing manifest file 'pip-egg-info/dionysus.egg-info/SOURCES.txt'
    warning: manifest_maker: standard file '-c' not found
 
    reading manifest file 'pip-egg-info/dionysus.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no files found matching '*' under directory '.'
    warning: no previously-included files matching '*' found under directory './.hg'
    warning: no previously-included files matching '*' found under directory './doc/_build'
    warning: no previously-included files matching '*' found under directory './dist'
    warning: no previously-included files found matching '.hgignore'
    warning: no previously-included files found matching '.hgsubtree'
    warning: no previously-included files found matching 'tags'
    warning: no previously-included files matching '*.orig' found under directory '.'
    writing manifest file 'pip-egg-info/dionysus.egg-info/SOURCES.txt'
  Source in /tmp/pip-install-IsduFR/dionysus has version 2.0.4, which satisfies requirement dionysus from https://files.pythonhosted.org/packages/e7/7c/9e5f6911dfac70ac62a544155f9e3b4436f20a8c4e8559aeb492381549c1/dionysus-2.0.4.tar.gz#sha256=e411396c63aa6838e414c18979d4d90a28fcc60ae1660389e6b777a43479bf40
Building wheels for collected packages: dionysus
  Created temporary directory: /tmp/pip-wheel-I26XHU
  Running setup.py bdist_wheel for dionysus ...   Destination directory: /tmp/pip-wheel-I26XHU
  Running command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-IsduFR/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-I26XHU --python-tag cp27
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-2.7
  creating build/lib.linux-x86_64-2.7/dionysus
  copying bindings/python/dionysus/_version.py -> build/lib.linux-x86_64-2.7/dionysus
  copying bindings/python/dionysus/__init__.py -> build/lib.linux-x86_64-2.7/dionysus
  copying bindings/python/dionysus/plot.py -> build/lib.linux-x86_64-2.7/dionysus
  running build_ext
  -- The C compiler identification is GNU 5.4.0
  -- The CXX compiler identification is GNU 5.4.0
  -- Check for working C compiler: /usr/bin/cc
  -- Check for working C compiler: /usr/bin/cc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- Check for working CXX compiler: /usr/bin/c++
  -- Check for working CXX compiler: /usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- Could NOT find Boost
  -- Found PythonInterp: /usr/bin/python (found version "2.7.12")
  -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so
  -- Performing Test HAS_CPP14_FLAG
  -- Performing Test HAS_CPP14_FLAG - Success
  -- pybind11 v2.2.0
  -- Performing Test HAS_FLTO
  -- Performing Test HAS_FLTO - Success
  -- LTO enabled
  CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
  Please set them or make sure they are set and tested correctly in the CMake files:
  Boost_INCLUDE_DIR (ADVANCED)
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python/pybind11
     used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python/pybind11
 
  -- Configuring incomplete, errors occurred!
  See also "/tmp/pip-install-IsduFR/dionysus/build/temp.linux-x86_64-2.7/CMakeFiles/CMakeOutput.log".
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/tmp/pip-install-IsduFR/dionysus/setup.py", line 97, in <module>
      zip_safe=False,
    File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
      dist.run_commands()
    File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
      self.run_command(cmd)
    File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/usr/lib/python2.7/dist-packages/wheel/bdist_wheel.py", line 179, in run
      self.run_command('build')
    File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
      self.distribution.run_command(command)
    File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/usr/lib/python2.7/distutils/command/build.py", line 128, in run
      self.run_command(cmd_name)
    File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
      self.distribution.run_command(command)
    File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/tmp/pip-install-IsduFR/dionysus/setup.py", line 39, in run
      self.build_extension(ext)
    File "/tmp/pip-install-IsduFR/dionysus/setup.py", line 64, in build_extension
      subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
    File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-IsduFR/dionysus', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-IsduFR/dionysus/build/lib.linux-x86_64-2.7', '-DPYTHON_EXECUTABLE=/usr/bin/python', '-Dbuild_examples=OFF', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1
error
  Failed building wheel for dionysus
  Running setup.py clean for dionysus
  Running command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-IsduFR/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" clean --all
  running clean
  removing 'build/temp.linux-x86_64-2.7' (and everything under it)
  removing 'build/lib.linux-x86_64-2.7' (and everything under it)
  'build/bdist.linux-x86_64' does not exist -- can't clean it
  'build/scripts-2.7' does not exist -- can't clean it
  removing 'build'
Failed to build dionysus
Installing collected packages: dionysus
  Created temporary directory: /tmp/pip-record-jmS7H0
  Running setup.py install for dionysus ...     Running command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-IsduFR/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-jmS7H0/install-record.txt --single-version-externally-managed --compile
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-2.7
    creating build/lib.linux-x86_64-2.7/dionysus
    copying bindings/python/dionysus/_version.py -> build/lib.linux-x86_64-2.7/dionysus
    copying bindings/python/dionysus/__init__.py -> build/lib.linux-x86_64-2.7/dionysus
    copying bindings/python/dionysus/plot.py -> build/lib.linux-x86_64-2.7/dionysus
    running build_ext
    -- The C compiler identification is GNU 5.4.0
    -- The CXX compiler identification is GNU 5.4.0
    -- Check for working C compiler: /usr/bin/cc
    -- Check for working C compiler: /usr/bin/cc -- works
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Detecting C compile features
    -- Detecting C compile features - done
    -- Check for working CXX compiler: /usr/bin/c++
    -- Check for working CXX compiler: /usr/bin/c++ -- works
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- Detecting CXX compile features
    -- Detecting CXX compile features - done
    -- Could NOT find Boost
    -- Found PythonInterp: /usr/bin/python (found version "2.7.12")
    -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so
    -- Performing Test HAS_CPP14_FLAG
    -- Performing Test HAS_CPP14_FLAG - Success
    -- pybind11 v2.2.0
    -- Performing Test HAS_FLTO
    -- Performing Test HAS_FLTO - Success
    -- LTO enabled
    CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
    Please set them or make sure they are set and tested correctly in the CMake files:
    Boost_INCLUDE_DIR (ADVANCED)
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python/pybind11
       used as include directory in directory /tmp/pip-install-IsduFR/dionysus/bindings/python/pybind11
 
    -- Configuring incomplete, errors occurred!
    See also "/tmp/pip-install-IsduFR/dionysus/build/temp.linux-x86_64-2.7/CMakeFiles/CMakeOutput.log".
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-IsduFR/dionysus/setup.py", line 97, in <module>
        zip_safe=False,
      File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
        dist.run_commands()
      File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/usr/lib/python2.7/dist-packages/setuptools/command/install.py", line 61, in run
        return orig.install.run(self)
      File "/usr/lib/python2.7/distutils/command/install.py", line 601, in run
        self.run_command('build')
      File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
        self.distribution.run_command(command)
      File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/usr/lib/python2.7/distutils/command/build.py", line 128, in run
        self.run_command(cmd_name)
      File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
        self.distribution.run_command(command)
      File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/tmp/pip-install-IsduFR/dionysus/setup.py", line 39, in run
        self.build_extension(ext)
      File "/tmp/pip-install-IsduFR/dionysus/setup.py", line 64, in build_extension
        subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
      File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-IsduFR/dionysus', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-IsduFR/dionysus/build/lib.linux-x86_64-2.7', '-DPYTHON_EXECUTABLE=/usr/bin/python', '-Dbuild_examples=OFF', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1
error
Cleaning up...
  Removing source in /tmp/pip-install-IsduFR/dionysus
Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-IsduFR/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-jmS7H0/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-IsduFR/dionysus/
Exception information:
Traceback (most recent call last):
  File "/home/ubuntu/.local/lib/python2.7/site-packages/pip/_internal/basecommand.py", line 228, in main
    status = self.run(options, args)
  File "/home/ubuntu/.local/lib/python2.7/site-packages/pip/_internal/commands/install.py", line 335, in run
    use_user_site=options.use_user_site,
  File "/home/ubuntu/.local/lib/python2.7/site-packages/pip/_internal/req/__init__.py", line 49, in install_given_reqs
    **kwargs
  File "/home/ubuntu/.local/lib/python2.7/site-packages/pip/_internal/req/req_install.py", line 779, in install
    spinner=spinner,
  File "/home/ubuntu/.local/lib/python2.7/site-packages/pip/_internal/utils/misc.py", line 698, in call_subprocess
    % (command_desc, proc.returncode, cwd))
InstallationError: Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-IsduFR/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-jmS7H0/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-IsduFR/dionysus/

Re: Error when building on windows

Connor Brennan <sharsnik@...>
 

I solved this issue by using MinGW as my compiler.

Thanks.

On Tue, Apr 10, 2018 at 4:22 PM, Connor Brennan <sharsnik@...> wrote:
I should also mention that I'm using MSVC 19.13.26129.0 as the compiler and I have Boost 1.66.0.

On Tue, Apr 10, 2018 at 4:20 PM, Dmitriy Morozov <dmitriy@...> wrote:
I'm afraid I don't use Windows, so it's difficult for me to debug this problem. If anyone on the list has successfully used Dionysus on Windows, I hope they speak up.

Dmitriy

On Tue, Apr 10, 2018 at 1:17 PM, <sharsnik@...> wrote:
I am building Dionysus on Windows 10 using vcpkg and python 3.6.5. I'm getting a variety of errors that I suspect all have the same cause. Here's an example of the errors I get when building filtration-persistence.exe. All examples give similar such errors.

\dionysus\include\dionysus\simplex.h(240): error C2244: 'dionysus::Simplex<Vertex_,T>::boundary_begin': unable to match function definition to an existing declaration 
\dionysus\include\dionysus\simplex.h(250): error C2244: 'dionysus::Simplex<Vertex_,T>::boundary_end': unable to match function definition to an existing declaration 
\dionysus\examples\filtration\filtration-persistence.cpp(48): error C2976: 'dionysus::RowReduction': too few template arguments 
\dionysus\examples\filtration\filtration-persistence.cpp(48): error C2514: 'dionysus::RowReduction': class has no constructors 
\dionysus\examples\filtration\filtration-persistence.cpp(49): error C3848: expression having type 'dionysus::RowReduction' would lose some const-volatile qualifiers in order to call 'void dionysus::RowReduction<Field_,Index_,Comparison_,Visitors...>::operator ()<Filtration>(const Filtration &)' 






--
-Connor Brennan
Fractal Entertainment




--
-Connor Brennan
Fractal Entertainment

Re: Error when building on windows

sharsnik@...
 

I should also mention that I'm using MSVC 19.13.26129.0 as the compiler and I have Boost 1.66.0.

On Tue, Apr 10, 2018 at 4:20 PM, Dmitriy Morozov <dmitriy@...> wrote:
I'm afraid I don't use Windows, so it's difficult for me to debug this problem. If anyone on the list has successfully used Dionysus on Windows, I hope they speak up.

Dmitriy

On Tue, Apr 10, 2018 at 1:17 PM, <sharsnik@...> wrote:
I am building Dionysus on Windows 10 using vcpkg and python 3.6.5. I'm getting a variety of errors that I suspect all have the same cause. Here's an example of the errors I get when building filtration-persistence.exe. All examples give similar such errors.

\dionysus\include\dionysus\simplex.h(240): error C2244: 'dionysus::Simplex<Vertex_,T>::boundary_begin': unable to match function definition to an existing declaration 
\dionysus\include\dionysus\simplex.h(250): error C2244: 'dionysus::Simplex<Vertex_,T>::boundary_end': unable to match function definition to an existing declaration 
\dionysus\examples\filtration\filtration-persistence.cpp(48): error C2976: 'dionysus::RowReduction': too few template arguments 
\dionysus\examples\filtration\filtration-persistence.cpp(48): error C2514: 'dionysus::RowReduction': class has no constructors 
\dionysus\examples\filtration\filtration-persistence.cpp(49): error C3848: expression having type 'dionysus::RowReduction' would lose some const-volatile qualifiers in order to call 'void dionysus::RowReduction<Field_,Index_,Comparison_,Visitors...>::operator ()<Filtration>(const Filtration &)' 






--
-Connor Brennan
Fractal Entertainment

Re: Error when building on windows

Dmitriy Morozov
 

I'm afraid I don't use Windows, so it's difficult for me to debug this problem. If anyone on the list has successfully used Dionysus on Windows, I hope they speak up.

Dmitriy

On Tue, Apr 10, 2018 at 1:17 PM, <sharsnik@...> wrote:
I am building Dionysus on Windows 10 using vcpkg and python 3.6.5. I'm getting a variety of errors that I suspect all have the same cause. Here's an example of the errors I get when building filtration-persistence.exe. All examples give similar such errors.

\dionysus\include\dionysus\simplex.h(240): error C2244: 'dionysus::Simplex<Vertex_,T>::boundary_begin': unable to match function definition to an existing declaration 
\dionysus\include\dionysus\simplex.h(250): error C2244: 'dionysus::Simplex<Vertex_,T>::boundary_end': unable to match function definition to an existing declaration 
\dionysus\examples\filtration\filtration-persistence.cpp(48): error C2976: 'dionysus::RowReduction': too few template arguments 
\dionysus\examples\filtration\filtration-persistence.cpp(48): error C2514: 'dionysus::RowReduction': class has no constructors 
\dionysus\examples\filtration\filtration-persistence.cpp(49): error C3848: expression having type 'dionysus::RowReduction' would lose some const-volatile qualifiers in order to call 'void dionysus::RowReduction<Field_,Index_,Comparison_,Visitors...>::operator ()<Filtration>(const Filtration &)' 



Error when building on windows

sharsnik@...
 

I am building Dionysus on Windows 10 using vcpkg and python 3.6.5. I'm getting a variety of errors that I suspect all have the same cause. Here's an example of the errors I get when building filtration-persistence.exe. All examples give similar such errors.

\dionysus\include\dionysus\simplex.h(240): error C2244: 'dionysus::Simplex<Vertex_,T>::boundary_begin': unable to match function definition to an existing declaration 
\dionysus\include\dionysus\simplex.h(250): error C2244: 'dionysus::Simplex<Vertex_,T>::boundary_end': unable to match function definition to an existing declaration 
\dionysus\examples\filtration\filtration-persistence.cpp(48): error C2976: 'dionysus::RowReduction': too few template arguments 
\dionysus\examples\filtration\filtration-persistence.cpp(48): error C2514: 'dionysus::RowReduction': class has no constructors 
\dionysus\examples\filtration\filtration-persistence.cpp(49): error C3848: expression having type 'dionysus::RowReduction' would lose some const-volatile qualifiers in order to call 'void dionysus::RowReduction<Field_,Index_,Comparison_,Visitors...>::operator ()<Filtration>(const Filtration &)' 


Re: Installation/Compilation problems Dionysus

Dmitriy Morozov
 

Both your compiler and Boost versions are too old. You need at least GCC 5.4 (you are using 4.8.5). And you need at least Boost 1.55 (you are using 1.54).

Dmitriy

On Sat, Mar 31, 2018 at 2:23 PM, Arne Roland <arneroland@...> wrote:
Hello,

I tried to install Dionysus 2 with pip and got an output with very
internal error messages. Am I doing something wrong?

Thank you for your help!

All the best
Arne Roland





Installation/Compilation problems Dionysus

Arne Roland
 

Hello,

I tried to install Dionysus 2 with pip and got an output with very
internal error messages. Am I doing something wrong?

Thank you for your help!

All the best
Arne Roland

Re: Persistent diagram of one-dimensional data

Mahdi Kooshkbaghi
 

Dear Dimitry,
Thank you very much. Even your short description solve my conceptual problem.
Best,
Mahdi

Re: Persistent diagram of one-dimensional data

Dmitriy Morozov
 

Hi Mahdi,

Below is an example that does what you want, I think. It boils down to generating the lower-star filtration of a piecewise-linear function whose values you give as a NumPy array [1]. The plot of the persistence diagram is missing the point at infinity, although the diagram itself (dgm[0]) has that point.


Dmitriy

import dionysus as d
import numpy as np
import matplotlib.pyplot as plt

a = np.array([10,4,7,3,9,2,12], dtype='f4')
plt.plot(a)
plt.show()

f = d.fill_freudenthal(a)
p = d.homology_persistence(f)
dgm = d.init_diagrams(p,f)

d.plot.plot_diagram(dgm[0], show=True)


On Tue, Mar 20, 2018 at 2:28 PM, <mahdik@...> wrote:
Dear all,
It could be more conceptual issue about the topic rather than software issue.
I wonder how can I generate persistent diagrams for the scalar field via Dionysus?
I have attached the figure from "Persistent homology survey by H. E. and J. H".
I am trying to understand and plot something similar.
Thanks,
Mahdi
PS: for two and more-dimensional data I can understand and play with package to get the persistence diagrams.


Persistent diagram of one-dimensional data

Mahdi Kooshkbaghi
 

Dear all,
It could be more conceptual issue about the topic rather than software issue.
I wonder how can I generate persistent diagrams for the scalar field via Dionysus?
I have attached the figure from "Persistent homology survey by H. E. and J. H".
I am trying to understand and plot something similar.
Thanks,
Mahdi
PS: for two and more-dimensional data I can understand and play with package to get the persistence diagrams.

Re: Error on pip install

Dmitriy Morozov
 

I think I'd need to see the "skipped 6710 bytes of output" to even attempt to guess. Currently, there is not much information there.

The fact that all this is happening under Java is also very suspicious.

On Mon, Mar 12, 2018 at 7:13 AM, <eric.a.bunch@...> wrote:
Hello, this may be outside of your purview, but I am trying to install dionysus on a databricks cluster, and keep getting an error. I have installed it locally a few times with no problems, but on databricks it gives me an error that I haven't been able to make sense of, and was wondering if you had any ideas on things to try. This is the error after trying to install from pypi

Error: java.lang.RuntimeException: Installation failed with message: Collecting dionysus Downloading dionysus-2.0.4.tar.gz (1.0MB) Building wheels for collected packag *** WARNING: skipped 6710 bytes of output *** alled to build the following extensions: dionysus ---------------------------------------- Failed building wheel for dionysus Command "/databricks/python3/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-drey1xhy/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-48un6qym-record/install-record.txt --single-version-externally-managed --compile --install-headers /databricks/python3/include/site/python3.5/dionysus" failed with error code 1 in /tmp/pip-build-drey1xhy/dionysus/

Any suggestions are welcome.


Error on pip install

eric.a.bunch@...
 

Hello, this may be outside of your purview, but I am trying to install dionysus on a databricks cluster, and keep getting an error. I have installed it locally a few times with no problems, but on databricks it gives me an error that I haven't been able to make sense of, and was wondering if you had any ideas on things to try. This is the error after trying to install from pypi

Error: java.lang.RuntimeException: Installation failed with message: Collecting dionysus Downloading dionysus-2.0.4.tar.gz (1.0MB) Building wheels for collected packag *** WARNING: skipped 6710 bytes of output *** alled to build the following extensions: dionysus ---------------------------------------- Failed building wheel for dionysus Command "/databricks/python3/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-drey1xhy/dionysus/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-48un6qym-record/install-record.txt --single-version-externally-managed --compile --install-headers /databricks/python3/include/site/python3.5/dionysus" failed with error code 1 in /tmp/pip-build-drey1xhy/dionysus/

Any suggestions are welcome.

Re: Constructing rips filtration using the distance matrix

Dmitriy Morozov
 

Hi Biraj,

The functionality is still there. It just doesn't like that the array entries are integers (it wants them to be floating point numbers). The easiest fix is to add ".astype('f4')" to your array:

dist_matrix = np.array([[0, 5, 4], [5, 0, 3], [4, 3, 0]]).astype('f4')
f = d.fill_rips(squareform(dist_matrix), 2, 1000)

Let me know if that works.

Best,
Dmitriy


On Tue, Feb 27, 2018 at 10:40 PM, biraj.pandey via Groups.Io <biraj.pandey@...> wrote:
Hi Dmitriy,

Is there anyway to construct a rips filtration using the distance matrix itself instead of the point cloud? In my specific case, I don't have the point cloud and only the distance matrix. I am having issues with the fill_rips function.

We had a conversation relating to this past summer (July 25th, 2017 to be exact).  I did a fresh install and it seems that the feature is gone.  Before I could do something like,

dist_matrix = np.array([[0, 5, 4], [5, 0, 3], [4, 3, 0]])
f = d.fill_rips(squareform(dist_matrix), 2, 1000)

Now, when I run that I get the error that says
RuntimeError: Unknown array dtype

Any chance you could bring the back? Or perhaps some workaround?

Best, 
Biraj


Constructing rips filtration using the distance matrix

biraj.pandey@...
 

Hi Dmitriy,

Is there anyway to construct a rips filtration using the distance matrix itself instead of the point cloud? In my specific case, I don't have the point cloud and only the distance matrix. I am having issues with the fill_rips function.

We had a conversation relating to this past summer (July 25th, 2017 to be exact).  I did a fresh install and it seems that the feature is gone.  Before I could do something like,

dist_matrix = np.array([[0, 5, 4], [5, 0, 3], [4, 3, 0]])
f = d.fill_rips(squareform(dist_matrix), 2, 1000)

Now, when I run that I get the error that says
RuntimeError: Unknown array dtype

Any chance you could bring the back? Or perhaps some workaround?

Best, 
Biraj