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Keck-DataReductionPipelines / MosfireDRP

http://keck-datareductionpipelines.github.io/MosfireDRP
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Issue when creating the conda environnement #145

Open NicolasLaporte opened 4 years ago

NicolasLaporte commented 4 years ago

Hi,

I got the following issue when creating my conda environnement, I am wondering if this is just not a repository issue :

`(base) nlaporte@nicolass-macbook-pro-2 J % conda env create KeckObservatory/mospy_2018_macos
Collecting package metadata (repodata.json): done Solving environment: failed

ResolvePackageNotFound:

Any idea how I can solve this ? Many thanks in advance

joshwalawender commented 4 years ago

Hi @NicolasLaporte , I will try to work up a new environment file and get that out later today.

-Josh

joshwalawender commented 4 years ago

@NicolasLaporte Try using this environment file (note this is a temporary link).

Install the environment using:

conda env create -f mospy.yaml

If it works for you, I'll put it in the repo for others to use.

-Josh

NicolasLaporte commented 4 years ago

Dear Josh,

Thanks for your quick answer. I can now create the mospy environment but when typing “mospy AutoDriver” I get the error “mospy: command not found”. I think there is just a link missing in the .yaml file to install the pipeline, no ?

Thanks. Nicolas

From: Josh Walawender notifications@github.com Reply to: Keck-DataReductionPipelines/MosfireDRP reply@reply.github.com Date: Friday, 4 September 2020 at 22:45 To: Keck-DataReductionPipelines/MosfireDRP MosfireDRP@noreply.github.com Cc: "Laporte, Nicolas" n.laporte@ucl.ac.uk, Mention mention@noreply.github.com Subject: Re: [Keck-DataReductionPipelines/MosfireDRP] Issue when creating the conda environnement (#145)

@NicolasLaportehttps://github.com/NicolasLaporte Try using this environment filehttps://www.dropbox.com/s/3eqkbtlqo0c7vw0/mospy.yaml?dl=0 (note this is a temporary link).

Install the environment using:

conda env create -f mospy.yaml

If it works for you, I'll put it in the repo for others to use.

-Josh

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Keck-DataReductionPipelines/MosfireDRP/issues/145#issuecomment-687405293, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIOQV4CB7NQCYFDGCRP7TLTSEFNZHANCNFSM4QX6GRFA.

NicolasLaporte commented 4 years ago

Please forget my last message…

I downloaded the MOSFIRE zip package, and I get the following issue when running “python setup.py install”

(mospy) nicolass-macbook-pro-2:MosfireDRP-master nlaporte$ python3.6 setup.py install

The requested path 'astropy_helpers' for importing astropy_helpers does not exist, or does not contain a copy of the astropy_helpers package. Attempting download instead.

Downloading astropy_helpers; run setup.py with the --offline option to force offline installation.

Traceback (most recent call last):

File "setup.py", line 18, in 

from astropy_helpers.setup_helpers import (

ModuleNotFoundError: No module named 'astropy_helpers.setup_helpers'

Best regards Nicolas

From: Josh Walawender notifications@github.com Reply to: Keck-DataReductionPipelines/MosfireDRP reply@reply.github.com Date: Friday, 4 September 2020 at 22:45 To: Keck-DataReductionPipelines/MosfireDRP MosfireDRP@noreply.github.com Cc: "Laporte, Nicolas" n.laporte@ucl.ac.uk, Mention mention@noreply.github.com Subject: Re: [Keck-DataReductionPipelines/MosfireDRP] Issue when creating the conda environnement (#145)

@NicolasLaportehttps://github.com/NicolasLaporte Try using this environment filehttps://www.dropbox.com/s/3eqkbtlqo0c7vw0/mospy.yaml?dl=0 (note this is a temporary link).

Install the environment using:

conda env create -f mospy.yaml

If it works for you, I'll put it in the repo for others to use.

-Josh

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Keck-DataReductionPipelines/MosfireDRP/issues/145#issuecomment-687405293, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIOQV4CB7NQCYFDGCRP7TLTSEFNZHANCNFSM4QX6GRFA.

NicolasLaporte commented 4 years ago

Dear Josh,

I solved the problem by doing a simple “pip install astropy-helpers==3.1“

Now it works perfectly,

Many thanks for your help,

Nicolas

From: "Laporte, Nicolas" n.laporte@ucl.ac.uk Date: Monday, 7 September 2020 at 08:02 To: Keck-DataReductionPipelines/MosfireDRP reply@reply.github.com, Keck-DataReductionPipelines/MosfireDRP MosfireDRP@noreply.github.com Cc: Mention mention@noreply.github.com Subject: Re: [Keck-DataReductionPipelines/MosfireDRP] Issue when creating the conda environnement (#145)

Please forget my last message…

I downloaded the MOSFIRE zip package, and I get the following issue when running “python setup.py install”

(mospy) nicolass-macbook-pro-2:MosfireDRP-master nlaporte$ python3.6 setup.py install

The requested path 'astropy_helpers' for importing astropy_helpers does not exist, or does not contain a copy of the astropy_helpers package. Attempting download instead.

Downloading astropy_helpers; run setup.py with the --offline option to force offline installation.

Traceback (most recent call last):

File "setup.py", line 18, in 

from astropy_helpers.setup_helpers import (

ModuleNotFoundError: No module named 'astropy_helpers.setup_helpers'

Best regards Nicolas

From: Josh Walawender notifications@github.com Reply to: Keck-DataReductionPipelines/MosfireDRP reply@reply.github.com Date: Friday, 4 September 2020 at 22:45 To: Keck-DataReductionPipelines/MosfireDRP MosfireDRP@noreply.github.com Cc: "Laporte, Nicolas" n.laporte@ucl.ac.uk, Mention mention@noreply.github.com Subject: Re: [Keck-DataReductionPipelines/MosfireDRP] Issue when creating the conda environnement (#145)

@NicolasLaportehttps://github.com/NicolasLaporte Try using this environment filehttps://www.dropbox.com/s/3eqkbtlqo0c7vw0/mospy.yaml?dl=0 (note this is a temporary link).

Install the environment using:

conda env create -f mospy.yaml

If it works for you, I'll put it in the repo for others to use.

-Josh

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Keck-DataReductionPipelines/MosfireDRP/issues/145#issuecomment-687405293, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIOQV4CB7NQCYFDGCRP7TLTSEFNZHANCNFSM4QX6GRFA.

monodera commented 3 years ago

I have the same issue on macOS 10.15.7 and conda 4.9.2. When I tried the updated mospy.yaml file above with conda env create -f mospy.yaml, I got the following error and the environment was not created. 

Collecting package metadata (repodata.json): done
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                                     /
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                                     |

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package numpy conflicts for:
ccdproc=1.3.0 -> astropy[version='>=1.0'] -> numpy[version='1.10.*|1.11.*|1.12.*|1.13.*|>=1.10|>=1.11|>=1.13|>=1.14|>=1.16.5,<2.0a0|>=1.16|>=1.19.4,<2.0a0|>=1.19|>=1.17|>=1.9|>=1.19.2,<2.0a0|>=1.16.6,<2.0a0|>=1.17.4,<2.0a0|>=1.14.6,<2.0a0|>=1.13.3,<2.0a0|>=1.11.3,<2.0a0|>=1.10.4,<2.0a0|>=1.9.3,<2.0a0|>=1.14.0,<2.0a0|>=1.13.*|>=1.14.*|1.9.*|>=1.18.5,<2.0a0|>=1.18.1,<2.0a0|>=1.15.1,<2.0a0']
ccdproc=1.3.0 -> numpy
astropy=2.0.3 -> numpy[version='>=1.9.3,<2.0a0']
scipy=1.0.0 -> numpy[version='>=1.9|>=1.9.3,<2.0a0']
numpy=1.13.3

Package scipy conflicts for:
ccdproc=1.3.0 -> reproject -> scipy[version='>=0.17|>=0.19|>=0.9|>=1.1']
scipy=1.0.0
ccdproc=1.3.0 -> scipy

Package llvm-openmp conflicts for:
ccdproc=1.3.0 -> scikit-image -> llvm-openmp[version='>=10.0.0|>=4.0.1']
numpy=1.13.3 -> mkl[version='>=2019.4,<2020.0a0'] -> llvm-openmp[version='>=10.0.0|>=10.0.1|>=11.0.0|>=9.0.1|>=9.0.0']

Package astropy conflicts for:
ccdproc=1.3.0 -> astropy[version='>=1.0']
ccdproc=1.3.0 -> astroscrappy -> astropy[version='>=1|>=2.0|>=3.2']
astropy=2.0.3

Package python conflicts for:
pyqt=5.6.0 -> sip=4.18 -> python=3.4
ccdproc=1.3.0 -> astropy[version='>=1.0'] -> python[version='3.4.*|>=2.7,<2.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|<3.6*']
python=3.6.3
ccdproc=1.3.0 -> python[version='2.7.*|3.5.*|3.6.*|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
astropy=2.0.3 -> numpy -> python[version='3.4.*|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0']
scipy=1.0.0 -> python[version='2.7.*|3.5.*|3.6.*|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0']
ipython=6.2.1 -> appnope -> python[version='2.7.*|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|3.4.*|>=3|>=3.5|>=3.7']
astropy=2.0.3 -> python[version='2.7.*|3.5.*|3.6.*|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0']
numpy=1.13.3 -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0']
pyqt=5.6.0 -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
ipython=6.2.1 -> python[version='3.5.*|3.6.*|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']
scipy=1.0.0 -> numpy[version='>=1.9'] -> python[version='3.4.*|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0']
numpy=1.13.3 -> mkl-service[version='>=2,<3.0a0'] -> python[version='>=3.7,<3.8.0a0|>=3.9,<3.10.0a0']

Package ca-certificates conflicts for:
ccdproc=1.3.0 -> python -> ca-certificates
astropy=2.0.3 -> python=2.7 -> ca-certificates
pyqt=5.6.0 -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
scipy=1.0.0 -> python=2.7 -> ca-certificates
numpy=1.13.3 -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
python=3.6.3 -> openssl=1.0 -> ca-certificates

Package libcxxabi conflicts for:
scipy=1.0.0 -> libcxx[version='>=4.0.1'] -> libcxxabi[version='4.0.1|4.0.1|8.0.0|8.0.0|8.0.0|8.0.0|8.0.1',build='hebd6815_0|1|0|4|3|2|hcfea43d_1']
python=3.6.3 -> libcxx[version='>=4.0.1'] -> libcxxabi[version='4.0.1|4.0.1|8.0.0|8.0.0|8.0.0|8.0.0|8.0.1',build='hebd6815_0|1|0|4|3|2|hcfea43d_1']
numpy=1.13.3 -> libcxx[version='>=4.0.1'] -> libcxxabi[version='4.0.1|4.0.1|8.0.0|8.0.0|8.0.0|8.0.0|8.0.1',build='hebd6815_0|1|0|4|3|2|hcfea43d_1']
pyqt=5.6.0 -> libcxx[version='>=4.0.1'] -> libcxxabi[version='4.0.1|4.0.1|8.0.0|8.0.0|8.0.0|8.0.0|8.0.1',build='hebd6815_0|1|0|4|3|2|hcfea43d_1']

Package libgfortran-ng conflicts for:
astropy=2.0.3 -> numpy -> libgfortran-ng[version='>=3.0']
scipy=1.0.0 -> numpy[version='>=1.9'] -> libgfortran-ng[version='>=3.0']
ccdproc=1.3.0 -> numpy -> libgfortran-ng[version='>=3.0']

Package python_abi conflicts for:
astropy=2.0.3 -> numpy -> python_abi[version='3.6.*|3.6|3.8.*|3.7.*|3.9.*',build='*_cp39|*_cp36m|*_cp37m|*_pypy36_pp73|*_cp38']
numpy=1.13.3 -> python[version='>=3.6,<3.7.0a0'] -> python_abi[version='3.6.*|3.6|3.7.*|3.9.*|3.8.*',build='*_cp39|*_cp36m|*_cp37m|*_pypy36_pp73|*_cp38']
ccdproc=1.3.0 -> astropy[version='>=1.0'] -> python_abi[version='3.6|3.6.*|3.7.*|3.8.*|3.9.*',build='*_pypy36_pp73|*_cp36m|*_cp37m|*_cp39|*_cp38']
scipy=1.0.0 -> numpy[version='>=1.9'] -> python_abi[version='3.6.*|3.6|3.8.*|3.7.*|3.9.*',build='*_cp39|*_cp36m|*_cp37m|*_pypy36_pp73|*_cp38']
pyqt=5.6.0 -> python[version='>=3.6,<3.7.0a0'] -> python_abi==3.6[build=*_pypy36_pp73]
ipython=6.2.1 -> appnope -> python_abi[version='2.7.*|3.6|3.6.*|3.7.*|3.9.*|3.8.*',build='*_pypy36_pp73|*_cp36m|*_cp37m|*_cp39|*_cp38|*_cp27m']

Package setuptools conflicts for:
ccdproc=1.3.0 -> astropy[version='>=1.0'] -> setuptools
ipython=6.2.1 -> pygments -> setuptools
python=3.6.3 -> pip -> setuptools
astropy=2.0.3 -> pytest -> setuptools[version='>=40.0']

Package liblapacke conflicts for:
scipy=1.0.0 -> blas=[build=mkl] -> liblapacke[version='3.8.0|3.9.0|3.9.0',build='3_openblas|7_openblas|8_openblas|11_openblas|13_openblas|15_openblas|17_openblas|4_mkl|6_mkl|7_mkl|8_mkl|19_mkl|20_mkl|21_mkl|18_mkl|16_mkl|15_mkl|14_mkl|13_mkl|12_mkl|11_mkl|10_mkl|9_mkl|5_mkl|16_openblas|14_openblas|12_openblas|10_openblas|9_openblas|6_openblas|5_openblas|4_openblas|2_openblas']
numpy=1.13.3 -> blas=[build=openblas] -> liblapacke[version='3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.9.0|3.9.0',build='6_mkl|7_mkl|8_mkl|12_mkl|13_mkl|15_mkl|19_mkl|3_openblas|10_openblas|11_openblas|12_openblas|13_openblas|17_openblas|16_openblas|15_openblas|14_openblas|9_openblas|8_openblas|7_openblas|6_openblas|5_openblas|4_openblas|2_openblas|21_mkl|20_mkl|18_mkl|16_mkl|14_mkl|11_mkl|10_mkl|9_mkl|5_mkl|4_mkl']

Package six conflicts for:
ccdproc=1.3.0 -> reproject -> six[version='>=1.4|>=1.7.3']
astropy=2.0.3 -> pytest -> six[version='>=1.10.0']
numpy=1.13.3 -> mkl-service[version='>=2,<3.0a0'] -> six
ipython=6.2.1 -> prompt_toolkit[version='>=1.0.4,<2.0.0'] -> six[version='>=1.9.0']

Package pathlib2 conflicts for:
ipython=6.2.1 -> pickleshare -> pathlib2
astropy=2.0.3 -> pytest -> pathlib2[version='>=2.2.0']

Package decorator conflicts for:
ccdproc=1.3.0 -> decorator
ipython=6.2.1 -> decorator

Package libgfortran5 conflicts for:
numpy=1.13.3 -> blas=[build=openblas] -> libgfortran5[version='>=9.3.0']
ccdproc=1.3.0 -> scipy -> libgfortran5[version='>=9.3.0']
scipy=1.0.0 -> blas=[build=mkl] -> libgfortran5[version='>=9.3.0']
Note that strict channel priority may have removed packages required for satisfiability.

Do you have any suggestions?

monodera commented 3 years ago

Apparently, this was caused by 

channel_priority: strict

in my ~/.condarc. When I commented out this line, I was able to create the environment.

mheida commented 3 years ago

@joshwalawender I'm getting the same issue when installing through Anaconda with conda env create KeckObservatory/mospy_2018_macos:

Solving environment: failed

ResolvePackageNotFound:

The mospy.yaml file you posted above is gone, could you post that again? Thanks!

joshwalawender commented 3 years ago

@mheida I've updated the environment spec on the anaconda cloud. Try running:

conda env create KeckObservatory/mospy

Note that I've removed the need to specify macOS or linux in the name. If that works, I'll update the installation instructions and add the environment file to the repository.

mheida commented 3 years ago

Thanks @joshwalawender! The installation seems to have worked, but I'm now getting a 'mospy: command not found' error when I try to run things and indeed there is no mospy executable in envs/mospy/bin (or anywhere else in envs/mospy as far as I can tell).

monodera commented 2 years ago

Recently, I found that the default setuptools installed along the mospy.yaml is >=58 (maybe with the latest conda-forge dependency), but it need to be earlier than that to install the MOSFIRE DRP.

https://stackoverflow.com/questions/69100275/error-while-downloading-the-requirements-using-pip-install-setup-command-use-2

Also, astropy-helpers should be explicitly installed with a specific version around 3.2.

Eventually, I used the following yaml file so that no additional package is required at the stage of the DRP installation.

name: mospy
channels:
  - conda-forge
  - defaults
dependencies:
  - ccdproc=1.3.0
  - numpy=1.13.3
  - scipy=1.0.0
  - python=3.6.3
  - astropy=2.0.3
  - pyqt=5.6.0
  - ipython=6.2.1
  - setuptools=57
  - pip
  - pip:
    - astropy-helpers==3.2.2
analuisagm commented 6 months ago

I share my experience.

conda env create KeckObservatory/mospy seems to work but then with python setup.py install I got an error The requested path 'astropy_helpers' for importing astropy_helpers does not exist, or does not contain a copy of the astropy_helpers package. Attempting download instead. Downloading astropy_helpers; run setup.py with the --offline option to force offline installation. Traceback (most recent call last): File "setup.py", line 18, in from astropy_helpers.setup_helpers import ( ModuleNotFoundError: No module named 'astropy_helpers.setup_helpers'

I fix it using:

pip install setuptools==57 pip install astropy-helpers==3.2.2

and running again: python setup.py install which now finished the process successfully.

Thank you to all for share the information.