Installation #5677
Install version 2.0.8
Description
History
#1 Updated by Albert van Eck over 3 years ago
- Subject changed from Install version 1.2.23 to Install version 2.0.8
#2 Updated by Albert van Eck about 3 years ago
- Estimated time changed from 2.00 h to 40.00 h
#3 Updated by Albert van Eck about 3 years ago
- Tracker changed from Support to Installation
#4 Updated by Albert van Eck about 3 years ago
- % Done changed from 20 to 70
- Status changed from New to In Progress
#5 Updated by Albert van Eck about 3 years ago
- Start date changed from 2020-05-14 to 2021-10-04
#6 Updated by Albert van Eck about 3 years ago
- Due date set to 2021-10-08
#7 Updated by Albert van Eck over 2 years ago
- Start date changed from 2021-10-04 to 2022-05-17
- Due date changed from 2021-10-08 to 2022-05-31
- File output.txt output.txt added
#8 Updated by Albert van Eck over 2 years ago
- % Done changed from 70 to 100
- Status changed from In Progress to Closed
#9 Updated by Albert van Eck over 2 years ago
(fermi_2.0.8) [root@node0518 ~]# /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python/envs/fermi_2.0.8/bin/python3.7 -m pip install "setuptools<58"
Collecting setuptools<58
Downloading setuptools-57.5.0-py3-none-any.whl (819 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 819.3/819.3 kB 7.8 MB/s eta 0:00:00
Installing collected packages: setuptools
Attempting uninstall: setuptools
Found existing installation: setuptools 62.3.2
Uninstalling setuptools-62.3.2:
Successfully uninstalled setuptools-62.3.2
Successfully installed setuptools-57.5.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
(fermi_2.0.8) [root@node0518 ~]# pip install "setuptools<58"
Requirement already satisfied: setuptools<58 in /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/envs/fermi_2.0.8/lib/python3.7/site-packages (57.5.0)
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
(fermi_2.0.8) [root@node0518 ~]# pip install pyds9
Requirement already satisfied: pyds9 in /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/envs/fermi_2.0.8/lib/python3.7/site-packages (1.8.1)
Requirement already satisfied: six in /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/envs/fermi_2.0.8/lib/python3.7/site-packages (from pyds9) (1.16.0)
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
(fermi_2.0.8) [root@node0518 ~]# pip install pyfits
Collecting pyfits
Using cached pyfits-3.5.tar.gz (1.7 MB)
Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/envs/fermi_2.0.8/lib/python3.7/site-packages (from pyfits) (1.21.6)
Building wheels for collected packages: pyfits
Building wheel for pyfits (setup.py) ... done
Created wheel for pyfits: filename=pyfits-3.5-cp37-cp37m-linux_x86_64.whl size=1035574 sha256=61c11af3f2490aca0c0b32620bb77385e99a5908f71e61baa8a2128217398dca
Stored in directory: /root/.cache/pip/wheels/08/e8/5b/05e3ed8ca223800d18334962514e593713e22452e45362ced9
Successfully built pyfits
Installing collected packages: pyfits
Successfully installed pyfits-3.5
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
(fermi_2.0.8) [root@node0518 ~]# conda config --add channels conda-forge
(fermi_2.0.8) [root@node0518 ~]# conda install -y cryptography pyopenssl urllib3
Collecting package metadata (current_repodata.json): done
Solving environment: done
current version: 4.9.2
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda- Package Plan ##
environment location: /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python/envs/fermi_2.0.8
added / updated specs:
- cryptography
- pyopenssl
- urllib3
The following packages will be downloaded:
package | build
---------------------------|-----------------
brotlipy-0.7.0 |py37h540881e_1004 342 KB conda-forge
cryptography-37.0.2 | py37h38fbfac_0 1.5 MB conda-forge
idna-3.3 | pyhd8ed1ab_0 55 KB conda-forge
pyopenssl-22.0.0 | pyhd8ed1ab_0 49 KB conda-forge
pysocks-1.7.1 | py37h89c1867_5 28 KB conda-forge
urllib3-1.26.9 | pyhd8ed1ab_0 100 KB conda-forge
------------------------------------------------------------
Total: 2.1 MBThe following NEW packages will be INSTALLED:
brotlipy conda-forge/linux-64::brotlipy-0.7.0-py37h540881e_1004
cryptography conda-forge/linux-64::cryptography-37.0.2-py37h38fbfac_0
idna conda-forge/noarch::idna-3.3-pyhd8ed1ab_0
pyopenssl conda-forge/noarch::pyopenssl-22.0.0-pyhd8ed1ab_0
pysocks conda-forge/linux-64::pysocks-1.7.1-py37h89c1867_5
urllib3 conda-forge/noarch::urllib3-1.26.9-pyhd8ed1ab_0Downloading and Extracting Packages
brotlipy-0.7.0 | 342 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
cryptography-37.0.2 | 1.5 MB | ################################################################################################################################################################################################################################################################################################################################# | 100%
idna-3.3 | 55 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
pysocks-1.7.1 | 28 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
pyopenssl-22.0.0 | 49 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
urllib3-1.26.9 | 100 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
You have PYTHONPATH set. This might interfere with the correct functioning of conda and the Fermi ST
(fermi_2.0.8) [root@node0518 ~]# python -c "import urllib3.contrib.pyopenssl; urllib3.contrib.pyopenssl.inject_into_urllib3()"
(fermi_2.0.8) [root@node0518 ~]# echo $?
0
(fermi_2.0.8) [root@node0518 ~]# conda install -y healpy ndg-httpsclient pyasn1 bz2file virtualenv cython ipython sympy pandas pathos readline fermiPy nb_conda
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: / failed with repodata from current_repodata.json, will retry with next repodata source.
CondaError: KeyboardInterrupt
^C
You have new mail in /var/spool/mail/root
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# alias conda='mambo '
(fermi_2.0.8) [root@node0518 ~]# conda install -y healpy ndg-httpsclient pyasn1 bz2file virtualenv cython ipython sympy pandas pathos readline fermiPy nb_conda
-bash: mambo: command not found
(fermi_2.0.8) [root@node0518 ~]# unalias conda
(fermi_2.0.8) [root@node0518 ~]# conda install mamba -c conda-forge
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: - failed with repodata from current_repodata.json, will retry with next repodata source.
CondaError: KeyboardInterrupt
^C
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# ^C
(fermi_2.0.8) [root@node0518 ~]# alias conda='mamba '
(fermi_2.0.8) [root@node0518 ~]# unalias conda
(fermi_2.0.8) [root@node0518 ~]# conda install mamba -c conda-forge
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done
current version: 4.9.2
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda- Package Plan ##
environment location: /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python/envs/fermi_2.0.8
added / updated specs:
- mamba
The following packages will be downloaded:
package | build
---------------------------|-----------------
charset-normalizer-2.0.12 | pyhd8ed1ab_0 35 KB conda-forge
conda-4.12.0 | py37h89c1867_0 1.0 MB conda-forge
conda-package-handling-1.8.1| py37h540881e_1 1.0 MB conda-forge
libarchive-3.5.1 | h3f442fb_1 1.6 MB conda-forge
libsolv-0.7.22 | h6239696_0 443 KB conda-forge
lzo-2.10 | h516909a_1000 314 KB conda-forge
mamba-0.15.3 | py37h7f483ca_0 741 KB conda-forge
pycosat-0.6.3 |py37h540881e_1010 107 KB conda-forge
reproc-14.2.3 | h7f98852_0 28 KB conda-forge
reproc-cpp-14.2.3 | h9c3ff4c_0 20 KB conda-forge
requests-2.27.1 | pyhd8ed1ab_0 53 KB conda-forge
ruamel_yaml-0.15.80 |py37h5e8e339_1006 270 KB conda-forge
------------------------------------------------------------
Total: 5.5 MBThe following NEW packages will be INSTALLED:
charset-normalizer conda-forge/noarch::charset-normalizer-2.0.12-pyhd8ed1ab_0
conda conda-forge/linux-64::conda-4.12.0-py37h89c1867_0
conda-package-han~ conda-forge/linux-64::conda-package-handling-1.8.1-py37h540881e_1
libarchive conda-forge/linux-64::libarchive-3.5.1-h3f442fb_1
libsolv conda-forge/linux-64::libsolv-0.7.22-h6239696_0
lzo conda-forge/linux-64::lzo-2.10-h516909a_1000
mamba conda-forge/linux-64::mamba-0.15.3-py37h7f483ca_0
pycosat conda-forge/linux-64::pycosat-0.6.3-py37h540881e_1010
reproc conda-forge/linux-64::reproc-14.2.3-h7f98852_0
reproc-cpp conda-forge/linux-64::reproc-cpp-14.2.3-h9c3ff4c_0
requests conda-forge/noarch::requests-2.27.1-pyhd8ed1ab_0
ruamel_yaml conda-forge/linux-64::ruamel_yaml-0.15.80-py37h5e8e339_1006Proceed ([y]/n)? y
Downloading and Extracting Packages
libarchive-3.5.1 | 1.6 MB | ################################################################################################################################################################################################################################################################################################################################# | 100%
lzo-2.10 | 314 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
reproc-14.2.3 | 28 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
conda-package-handli | 1.0 MB | ################################################################################################################################################################################################################################################################################################################################# | 100%
requests-2.27.1 | 53 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
libsolv-0.7.22 | 443 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
pycosat-0.6.3 | 107 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
reproc-cpp-14.2.3 | 20 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
ruamel_yaml-0.15.80 | 270 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
conda-4.12.0 | 1.0 MB | ################################################################################################################################################################################################################################################################################################################################# | 100%
charset-normalizer-2 | 35 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
mamba-0.15.3 | 741 KB | ################################################################################################################################################################################################################################################################################################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
You have PYTHONPATH set. This might interfere with the correct functioning of conda and the Fermi ST
(fermi_2.0.8) [root@node0518 ~]# alias conda='mamba '
You have new mail in /var/spool/mail/root
(fermi_2.0.8) [root@node0518 ~]# pip install "setuptools<58"
Requirement already satisfied: setuptools<58 in /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages (50.3.1.post20201107)
(fermi_2.0.8) [root@node0518 ~]# pip install pyds9
Processing ./.cache/pip/wheels/98/72/08/5741556191721ab31dff3bd5e31d2536cd86d9baa10e98f30e/pyds9-1.8.1-py3-none-any.whl
Requirement already satisfied: six in /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages (from pyds9) (1.15.0)
Installing collected packages: pyds9
Successfully installed pyds9-1.8.1
(fermi_2.0.8) [root@node0518 ~]# pip install pyfits
Processing ./.cache/pip/wheels/08/e8/5b/05e3ed8ca223800d18334962514e593713e22452e45362ced9/pyfits-3.5-cp37-cp37m-linux_x86_64.whl
Collecting numpy
Downloading numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
|████████████████████████████████| 15.7 MB 14.4 MB/s
Installing collected packages: numpy, pyfits
Successfully installed numpy-1.21.6 pyfits-3.5
(fermi_2.0.8) [root@node0518 ~]# conda config --add channels conda-forge
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╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝mamba (0.15.3) supported by @QuantStackGitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack█████████████████████████████████████████████████████████████
Currently, only install, create, list, search, run, info and clean are supported through mamba.
(fermi_2.0.8) [root@node0518 ~]# conda install -y cryptography pyopenssl urllib3
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/ / \____/ `
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██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝mamba (0.15.3) supported by @QuantStackGitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack█████████████████████████████████████████████████████████████
Looking for: ['cryptography', 'pyopenssl', 'urllib3']
pkgs/main/noarch [====================] (00m:00s) Done
pkgs/r/linux-64 [====================] (00m:00s) Done
pkgs/r/noarch [====================] (00m:00s) Done
pkgs/main/linux-64 [====================] (00m:01s) Done
conda-forge/noarch [====================] (00m:03s) Done
conda-forge/linux-64 [====================] (00m:07s) Done
Pinned packages:
- python 3.7.*
Transaction
Prefix: /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python/envs/fermi_2.0.8All requested packages already installed(fermi_2.0.8) [root@node0518 ~]# python -c "import urllib3.contrib.pyopenssl; urllib3.contrib.pyopenssl.inject_into_urllib3()"
(fermi_2.0.8) [root@node0518 ~]# conda install -y healpy ndg-httpsclient pyasn1 bz2file virtualenv cython ipython sympy pandas pathos readline fermiPy nb_conda
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/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \_
/ / \_/ \_/ \_/ \ o \__,
/ / \____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
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██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝mamba (0.15.3) supported by @QuantStackGitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack█████████████████████████████████████████████████████████████
Looking for: ['healpy', 'ndg-httpsclient', 'pyasn1', 'bz2file', 'virtualenv', 'cython', 'ipython', 'sympy', 'pandas', 'pathos', 'readline', 'fermipy', 'nb_conda']
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
pkgs/main/linux-64 [====================] (00m:00s) No change
pkgs/main/noarch [====================] (00m:00s) No change
pkgs/r/linux-64 [====================] (00m:00s) No change
pkgs/r/noarch [====================] (00m:00s) No change
Pinned packages:
- python 3.7.*
Transaction
Prefix: /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python/envs/fermi_2.0.8Updating specs:- healpy
- ndg-httpsclient
- pyasn1
- bz2file
- virtualenv
- cython
- ipython
- sympy
- pandas
- pathos
- readline
- fermipy
- nb_conda
- ca-certificates
- certifi
- opensslPackage Version Build Channel Size
───────────────────────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────────────────────+ bz2file 0.98 py_0 conda-forge/noarch 9 KB
+ cython 0.29.30 py37hd23a5d3_0 conda-forge/linux-64 2 MB
+ dill 0.3.5.1 pyhd8ed1ab_0 conda-forge/noarch 71 KB
+ distlib 0.3.4 pyhd8ed1ab_0 conda-forge/noarch 371 KB
+ fermipy 1.0.1 py37h6531663_1 conda-forge/linux-64 29 MB
+ filelock 3.7.0 pyhd8ed1ab_0 conda-forge/noarch 12 KB
+ gammapy 0.18.2 py37h5e8e339_0 conda-forge/linux-64 1019 KB
+ gmp 6.2.1 h58526e2_0 conda-forge/linux-64 806 KB
+ gmpy2 2.1.2 py37h025e8b9_0 conda-forge/linux-64 216 KB
+ healpy 1.15.0 py37hd0552aa_2 conda-forge/linux-64 4 MB
+ mpc 1.2.1 h9f54685_0 conda-forge/linux-64 106 KB
+ mpfr 4.1.0 h9202a9a_1 conda-forge/linux-64 3 MB
+ mpmath 1.2.1 pyhd8ed1ab_0 conda-forge/noarch 437 KB
+ multiprocess 0.70.12.2 py37h540881e_2 conda-forge/linux-64 184 KB
+ nb_conda 2.2.1 py37h89c1867_4 conda-forge/linux-64 36 KB
+ nb_conda_kernels 2.3.1 py37h89c1867_1 conda-forge/linux-64 27 KB
+ ndg-httpsclient 0.5.1 py_1 conda-forge/noarch 26 KB
+ pathos 0.2.8 pyhd8ed1ab_0 conda-forge/noarch 49 KB
+ platformdirs 2.5.1 pyhd8ed1ab_0 conda-forge/noarch 15 KB
+ pox 0.3.1 pyhd8ed1ab_0 conda-forge/noarch 24 KB
+ ppft 1.7.6.5 pyhd8ed1ab_0 conda-forge/noarch 32 KB
+ pyasn1 0.4.8 py_0 conda-forge/noarch 53 KB
+ pydantic 1.9.1 py37h540881e_0 conda-forge/linux-64 2 MB
+ pytest-runner 6.0.0 pyhd8ed1ab_0 conda-forge/noarch 11 KB
+ regions 0.5 py37h5e8e339_1 conda-forge/linux-64 295 KB
+ sympy 1.10.1 py37h89c1867_0 conda-forge/linux-64 12 MB
+ virtualenv 20.14.1 py37h89c1867_0 conda-forge/linux-64 8 MBSummary:Install: 27 packagesTotal download: 63 MB───────────────────────────────────────────────────────────────────────────────────
Finished pyasn1 (00m:00s) 53 KB 168 KB/s
Finished dill (00m:00s) 71 KB 223 KB/s
Finished gmp (00m:00s) 806 KB 2 MB/s
Finished bz2file (00m:00s) 9 KB 17 KB/s
Finished pox (00m:00s) 24 KB 48 KB/s
Finished ppft (00m:00s) 32 KB 63 KB/s
Finished ndg-httpsclient (00m:00s) 26 KB 41 KB/s
Finished filelock (00m:00s) 12 KB 18 KB/s
Finished multiprocess (00m:00s) 184 KB 222 KB/s
Finished nb_conda (00m:00s) 36 KB 42 KB/s
Finished pytest-runner (00m:00s) 11 KB 11 KB/s
Finished pydantic (00m:00s) 2 MB 2 MB/s
Finished distlib (00m:00s) 371 KB 377 KB/s
Finished sympy (00m:00s) 12 MB 15 MB/s
Finished cython (00m:00s) 2 MB 2 MB/s
Finished mpc (00m:00s) 106 KB 92 KB/s
Finished mpmath (00m:00s) 437 KB 364 KB/s
Finished platformdirs (00m:00s) 15 KB 9 KB/s
Finished gmpy2 (00m:00s) 216 KB 112 KB/s
Finished fermipy (00m:01s) 29 MB 19 MB/s
Finished healpy (00m:00s) 4 MB 2 MB/s
Finished regions (00m:00s) 295 KB 126 KB/s
Finished pathos (00m:00s) 49 KB 20 KB/s
Finished nb_conda_kernels (00m:00s) 27 KB 10 KB/s
Finished mpfr (00m:00s) 3 MB 987 KB/s
Finished gammapy (00m:01s) 1019 KB 246 KB/s
Finished virtualenv (00m:07s) 8 MB 977 KB/s
Downloading [====================================================================================================] (01m:04s) 7.24 MB/s
Extracting [================================================================================================> ] (01m:03s) 26 / 27
if not haveBase: raise getopt.GetoptError("Must specify basename, printing help.")
- print "Creating model map"
+ print("Creating model map")
qP = quickPlot(basename, True)
qP.createModelMap(modelFile)
return
elif opt in ('-r', '--residmap'):
if not haveBase: raise getopt.GetoptError("Must specify basename, printing help.")
- print "Creating residual map"
+ print("Creating residual map")
qP = quickPlot(basename,True)
qP.createResidMap()
return
elif opt in ('-s','--sigmap'):
if not haveBase: raise getopt.GetoptError("Must specify basename, printing help.")
- print "Creating significance map"
+ print("Creating significance map")
qP = quickPlot(basename,True)
qP.createSigMap()
return
elif opt in ('-p','--plot'):
if not haveBase: raise getopt.GetoptError("Must specify basename, printing help.")
- print "Plotting all maps"
+ print("Plotting all maps")
qP = quickPlot(basename, True)
qP.plotMaps()
return
elif opt in ('-P', '--Plot'):
if not haveBase: raise getopt.GetoptError("Must specify basename, printing help.")
- print "Creating all maps and then plotting them"
+ print("Creating all maps and then plotting them")
qP = quickPlot(basename, True)
qP.runAll(modelFile,True)
if not opts: raise getopt.GetoptError("Must specify an option, printing help.")except getopt.error as e:
- print "Command Line Error: " + e.msg
+ print("Command Line Error: " + e.msg)
printCLIHelp()if name == '__main__': cli()
RefactoringTool: Files that were modified:
RefactoringTool: ./quickPlot.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored ./quickUtils.py
--- ./quickUtils.py (original)
+++ ./quickUtils.py (refactored)
@ -10,7 +10,7 @
import os
import logging
import math
-import ConfigParser
+import configparser
import numpy as npfrom gt_apps import *
@ -56,12 +56,12 @basename = commonDictionary['base']- config = ConfigParser.RawConfigParser()
+ config = configparser.RawConfigParser()
config.read(basename+'.cfg')
if(not config.has_section('common')):
config.add_section('common')
- for variable, value in commonDictionary.iteritems():
+ for variable, value in commonDictionary.items():
config.set('common', variable, value)
quickLogger.info("wrote common config to "+basename+".cfg.")
@ -70,7 +70,7 @
quickLogger.info("quickAnalysis config exists, overwriting...")
else:
config.add_section('quickAnalysis')
- for variable, value in analysisDictionary.iteritems():
+ for variable, value in analysisDictionary.items():
config.set('quickAnalysis', variable, value)
quickLogger.info("wrote quickAnalysis config to "+basename+".cfg.")
@ -79,7 +79,7 @
quickLogger.info("quickLike config exists, overwriting...")
else:
config.add_section('quickLike')
- for variable, value in likelihoodDictionary.iteritems():
+ for variable, value in likelihoodDictionary.items():
config.set('quickLike', variable, value)
quickLogger.info("wrote quickLikeconfig to "+basename+".cfg.")
@ -88,7 +88,7 @
quickLogger.info("quickPlot config exists, overwriting...")
else:
config.add_section('quickPlot')
- for variable, value in plotDictionary.iteritems():
+ for variable, value in plotDictionary.items():
config.set('quickPlot', variable, value)
quickLogger.info("wrote quickPlot config to "+basename+".cfg.")
@ -97,7 +97,7 @
quickLogger.info("quickCurve config exists, overwriting...")
else:
config.add_section('quickCurve')
- for variable, value in curveDictionary.iteritems():
+ for variable, value in curveDictionary.items():
config.set('quickCurve', variable, value)
quickLogger.info("wrote quickCurve config to "+basename+".cfg.")
@ -120,7 +120,7 @
try:
checkForFiles(quickLogger,[basename+".cfg"])
quickLogger.info('Reading from config file ('+basename+'.cfg)')
- config = ConfigParser.RawConfigParser()
+ config = configparser.RawConfigParser()
config.read(basename+'.cfg')
if(config.has_section('common')):
@ -244,7 +244,7 @
AppCommand.run(print_command=printCmd)
quickLogger.info(AppCommand.command())
else:
- print AppCommand.command()
+ print(AppCommand.command())def runModel(quickLogger,
RefactoringTool: Files that were modified:
RefactoringTool: ./quickUtils.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored ./setup.py
--- ./setup.py (original)
+++ ./setup.py (refactored)
@ -23,9 +23,9 @
fermi_dir = os.environ.get("FERMI_DIR")if fermi_dir:
- print "The Fermi Science tools seem to be set up."
+ print("The Fermi Science tools seem to be set up.")
else:
- print "The Fermi Science tools are not set up."
+ print("The Fermi Science tools are not set up.")
sys.exit()setup(name='LATAnalysisScripts',
RefactoringTool: Files that were modified:
RefactoringTool: ./setup.py
(fermi_2.0.8) [root@node0518 LATAnalysisScripts-master]# python setup.py install
The Fermi Science tools seem to be set up.
running install
running build
running build_py
copying quickUtils.py > build/lib
copying quickAnalysis.py -> build/lib
copying quickLike.py -> build/lib
copying quickPlot.py -> build/lib
copying quickCurve.py -> build/lib
copying make2FGLxml.py -> build/lib
running install_lib
copying build/lib/quickUtils.py.bak -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages
copying build/lib/quickAnalysis.py.bak -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages
copying build/lib/quickLike.py.bak -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages
copying build/lib/quickPlot.py.bak -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages
copying build/lib/make2FGLxml.py.bak -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages
copying build/lib/quickUtils.py -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages
copying build/lib/quickAnalysis.py -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages
copying build/lib/quickLike.py -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages
copying build/lib/quickPlot.py -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages
copying build/lib/quickCurve.py -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages
copying build/lib/make2FGLxml.py -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages
byte-compiling /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages/quickUtils.py to quickUtils.cpython-37.pyc
byte-compiling /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages/quickAnalysis.py to quickAnalysis.cpython-37.pyc
byte-compiling /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages/quickLike.py to quickLike.cpython-37.pyc
byte-compiling /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages/quickPlot.py to quickPlot.cpython-37.pyc
Sorry: TabError: inconsistent use of tabs and spaces in indentation (quickPlot.py, line 367)
byte-compiling /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages/quickCurve.py to quickCurve.cpython-37.pyc
byte-compiling /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages/make2FGLxml.py to make2FGLxml.cpython-37.pyc
running install_data
creating /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python/envs/fermi_2.0.8/share/fermitools/bin
copying scripts/quickAnalysis -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python/envs/fermi_2.0.8/share/fermitools/bin
copying scripts/quickLike -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python/envs/fermi_2.0.8/share/fermitools/bin
copying scripts/quickPlot -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python/envs/fermi_2.0.8/share/fermitools/bin
copying scripts/quickCurve -> /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python/envs/fermi_2.0.8/share/fermitools/bin
running install_egg_info
Writing /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages/LATAnalysisScripts-0.2.0-py3.7.egg-info
(fermi_2.0.8) [root@node0518 LATAnalysisScripts-master]# popd
/scratch/vanecka/build/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0
(fermi_2.0.8) [root@node0518 2.0.8_gcc_9.3.0]# cd $APP_TMP
(fermi_2.0.8) [root@node0518 2.0.8_gcc_9.3.0]# wget https://github.com/kialio/gtapps_mp/archive/master.zip -O gtapps_mp-master.zip
--2022-05-24 16:10:52- https://github.com/kialio/gtapps_mp/archive/master.zip
Connecting to 172.31.1.254:3128... connected.
Proxy request sent, awaiting response... 301 Moved Permanently
Location: https://github.com/fermiPy/gtapps_mp/archive/master.zip [following]
--2022-05-24 16:10:53-- https://github.com/fermiPy/gtapps_mp/archive/master.zip
Connecting to 172.31.1.254:3128... connected.
Proxy request sent, awaiting response... 302 Found
Location: https://codeload.github.com/fermiPy/gtapps_mp/zip/refs/heads/master [following]
--2022-05-24 16:10:54-- https://codeload.github.com/fermiPy/gtapps_mp/zip/refs/heads/master
Connecting to 172.31.1.254:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: unspecified [application/zip]
Saving to: ‘gtapps_mp-master.zip’[ <=> ] 20,302 112KB/s in 0.2s2022-05-24 16:10:55 (112 KB/s) - ‘gtapps_mp-master.zip’ saved [20302]
(fermi_2.0.8) [root@node0518 2.0.8_gcc_9.3.0]# unzip gtapps_mp-master.zip
Archive: gtapps_mp-master.zip
b8b67db78d889c5a0a8ef93afbbf5aad5f17f439
replace gtapps_mp-master/.gitignore? [y]es, [n]o, [A]ll, [N]one, [r]ename: A
extracting: gtapps_mp-master/.gitignore
inflating: gtapps_mp-master/LICENSE
inflating: gtapps_mp-master/MANIFEST
inflating: gtapps_mp-master/README
inflating: gtapps_mp-master/gtapps_mp/__init__.py
inflating: gtapps_mp-master/gtapps_mp/gtdiffrsp_mp.py
inflating: gtapps_mp-master/gtapps_mp/gtexpmap_mp.py
inflating: gtapps_mp-master/gtapps_mp/gtltcube_mp.py
inflating: gtapps_mp-master/gtapps_mp/gtsrcmaps_mp.py
inflating: gtapps_mp-master/gtapps_mp/gttsmap_mp.py
inflating: gtapps_mp-master/gtapps_mp/utils.py
extracting: gtapps_mp-master/setup.cfg
inflating: gtapps_mp-master/setup.py
(fermi_2.0.8) [root@node0518 2.0.8_gcc_9.3.0]# pushd gtapps_mp-master/
/scratch/vanecka/build/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/gtapps_mp-master /scratch/vanecka/build/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0
(fermi_2.0.8) [root@node0518 gtapps_mp-master]# find . name "*.py" -exec 2to3 -w {} \; ./gtapps_mp/gtdiffrsp_mp.py (original)
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: No changes to ./gtapps_mp/__init__.py
RefactoringTool: Files that need to be modified:
RefactoringTool: ./gtapps_mp/__init__.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored ./gtapps_mp/gtdiffrsp_mp.py
--
+++ ./gtapps_mp/gtdiffrsp_mp.py (refactored)@ -21,7 +21,7 @
name of the created event file which can be combined with other
files and/or deleted later.'''
- print "Starting calculation on interval {} to {}".format(times0,times1)
+ print("Starting calculation on interval {} to {}".format(times0,times1))
osfilehandle,outfilename = tempfile.mkstemp(suffix=".fits")
filter['rad'] = "INDEF"
@ -47,7 +47,7 @
diffResps['irfs'] = times[5]
diffResps['chatter'] = 0
diffResps.run(print_command=False)
- print "Completed calculation of interval {} to {}".format(times[0],times[1])
+ print("Completed calculation of interval {} to {}".format(times[0],times[1]))
return outfilenamedef eventsum(filenames, Outfile, SaveTemp):
@ -83,10 +83,10 @
filter.run(print_command=False)if SaveTemp:
- print "Did not delete the following temporary files:"
- print filenames
+ print("Did not delete the following temporary files:")
+ print(filenames)
else:
- print "Deleting temporary files..."
+ print("Deleting temporary files...")
for filename in filenames:
os.remove(filename)@ -97,7 +97,7 @
and splits the time into chunks. It then submits jobs based upon
those start and stop times.'''
- print "Opening event file to determine break points..."
+ print("Opening event file to determine break points...")
hdulist = pyfits.open(EVFile)
tstart = hdulist0.header['TSTART']
tstop = hdulist0.header['TSTOP']@ -112,9 +112,9 @
pool = Pool(processes=bins)
times = np.array([starts,stops,scfiles,evfiles,srcmdls,irfs])
- print "Spawning {} jobs...".format(bins)
+ print("Spawning {} jobs...".format(bins))
tempfilenames = pool.map(diffrsp,times.transpose())
- print "Combining temporary files..."
+ print("Combining temporary files...")
eventsum(tempfilenames, OutFile, SaveTemp)
def cli():
RefactoringTool: Files that were modified:
RefactoringTool: ./gtapps_mp/gtdiffrsp_mp.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored ./gtapps_mp/gtexpmap_mp.py
--- ./gtapps_mp/gtexpmap_mp.py (original)
+++ ./gtapps_mp/gtexpmap_mp.py (refactored)
@ -18,10 +18,10 @
srcrad and nenergies. This function creates a temporary file for
the output and returns that file's name.'''- print "Starting calculation of region {},{} to {},{}".format(square0[0][0],
+ print("Starting calculation of region {},{} to {},{}".format(square0[0][0],
square0[1][0],
square0[0][1],
- square0[1][1])
+ square0[1][1]))
osfilehandle,outfilename = tempfile.mkstemp(suffix=".fits")
expMap['nlongmin'] = "{:,.0f}".format(float(square0[0][0]))
expMap['nlongmax'] = "{:,.0f}".format(float(square0[0][1]))@ -39,10 +39,10 @
expMap['submap'] = "yes"
expMap['chatter'] = 0
expMap.run(print_command=False)
- print "Completed calculation of region {},{} to {},{}".format(square0[0][0],
+ print("Completed calculation of region {},{} to {},{}".format(square0[0][0],
square0[1][0],
square0[0][1],
- square0[1][1])
+ square0[1][1]))
return outfilename@ -65,10 +65,10 @
for expmap_file in expmap_files: expmap_file.close()
if SaveTemp:
- print "Did not delete the following temporary files:"
- print filenames
+ print("Did not delete the following temporary files:")
+ print(filenames)
else:
- print "Deleting temporary files..."
+ print("Deleting temporary files...")
for filename in filenames:
os.remove(filename)@ -82,7 +82,7 @
bins = xbins*ybins
if np.mod(nlong,xbins) or np.mod(nlat,ybins):
- print "The number of x and y bins must fit evenly into the number of long or lat points."
+ print("The number of x and y bins must fit evenly into the number of long or lat points.")
returnstepx = nlong/xbins
@ -97,9 +97,9 @
SQ = [(row, SCFile,EVFile,ExpCube,nlong,nlat,IRF,srcrad,nenergy) for row in pairs]pool = Pool(processes=bins)
- print "Spawning {} jobs...".format(bins)
+ print("Spawning {} jobs...".format(bins))
filenames = pool.map(expmap,SQ)
- print "Combining temporary files..."
+ print("Combining temporary files...")
expsum(filenames, OutFile, SaveTemp)def cli():
RefactoringTool: Files that were modified:
RefactoringTool: ./gtapps_mp/gtexpmap_mp.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored ./gtapps_mp/gtltcube_mp.py
--- ./gtapps_mp/gtltcube_mp.py (original)
+++ ./gtapps_mp/gtltcube_mp.py (refactored)
@ -22,7 +22,7 @
created ltcube file which can be combined with other files and/or
deleted later.'''- print "Starting calculation on interval {} to {}".format(times0,times1)
+ print("Starting calculation on interval {} to {}".format(times0,times1))
if times3 != '':
evfile = tempfile.NamedTemporaryFile(suffix=".fits")
filter['ra']="INDEF" @ -59,7 +59,7 @
expCube['zmax'] = times4
expCube['chatter'] = 0
expCube.run(print_command=True)
- print "Completed calculation on interval {} to {}".format(times0,times1)
+ print("Completed calculation on interval {} to {}".format(times0,times1))
return outfilename
@ -83,10 +83,10 @
"outfile="+Outfile])
if SaveTemp:
- print "Did not delete the following temporary files:"
- print filenames
- else:
- print "Deleting temporary files..."
+ print("Did not delete the following temporary files:")
+ print(filenames)
+ else:
+ print("Deleting temporary files...")
for filename in filenames:
os.remove(filename)@ -107,15 +107,15 @
gti_data = evfile2.data
if tmin == 0:
- print "Determining start and stop times from the event file..."
+ print("Determining start and stop times from the event file...")
tstart = evfile[0].header['TSTART']
tstop = evfile[0].header['TSTOP']
else:
- print "Using user defined tmin and tmax..."
+ print("Using user defined tmin and tmax...")
tstart = tmin
tstop = tmax- print "Opening SC file to determine break points..."
+ print("Opening SC file to determine break points...")
hdulist = pyfits.open(SCFile, mode='readonly')
scdata = hdulist1.data
hdulist.close()@ -126,7 +126,7 @
redo = True
if EVFile !="":
- print "Checking for good times in the event file..."
+ print("Checking for good times in the event file...")
while redo:
redo = False
scstartssplit = np.array_split(scstart[time_filter],int(bins))
@ -141,42 +141,42 @if EVFile != "":
for interval in zip(starts,stops):
- if verbose: print "Looking at interval",interval[0],"to",interval[1]
+ if verbose: print("Looking at interval",interval[0],"to",interval[1])
good_times = False
#grrrr. some bug in pyfits doesn't let me do this the python way...
for gti_i in range(len(gti_data)):
if(not good_times):
- if verbose: print " Checking gti",gti_data[gti_i]['START'],"to",gti_data[gti_i]['STOP']
+ if verbose: print(" Checking gti",gti_data[gti_i]['START'],"to",gti_data[gti_i]['STOP'])
gti_starts = interval[0] <= gti_data[gti_i]['START'] <= interval[1]
gti_stops = interval[0] <= gti_data[gti_i]['STOP'] <= interval[1]
- if verbose: print " Does this gti start inside this interval? ", gti_starts
- if verbose: print " Does this gti stop inside this interval? ", gti_stops
+ if verbose: print(" Does this gti start inside this interval? ", gti_starts)
+ if verbose: print(" Does this gti stop inside this interval? ", gti_stops)
good_times = gti_starts or gti_stops
- if verbose: print
+ if verbose: print()- if verbose: print " Are there good times inside this interval? ", good_times
+ if verbose: print(" Are there good times inside this interval? ", good_times)
if not good_times:
redo = True
- if verbose: print
+ if verbose: print()
if redo:
if bins <= 1:
- print "No good time intervals found. Bailing..."
+ print("No good time intervals found. Bailing...")
sys.exit(1)
- print "One (or more) of the slices doesn't have a GTI."
- print "Reducing the number of threads from ",bins,"to",bins-1
+ print("One (or more) of the slices doesn't have a GTI.")
+ print("Reducing the number of threads from ",bins,"to",bins-1)
bins -= 1scfiles = [SCFile for st in scstartssplit]
evfiles = [EVFile for st in scstartssplit]
- print "EVFiles:",evfiles
+ print("EVFiles:",evfiles)
zmaxes = [zmax for st in scstartssplit]pool = Pool(processes=bins)
times = np.array([starts,stops,scfiles,evfiles,zmaxes])
- print "Spawning {} jobs...".format(bins)
+ print("Spawning {} jobs...".format(bins))
tempfilenames = pool.map(ltcube,times.transpose())
- print "Combining temporary files..."
+ print("Combining temporary files...")
ltsum(tempfilenames, OutFile, SaveTemp)def cli():
RefactoringTool: Files that were modified:
RefactoringTool: ./gtapps_mp/gtltcube_mp.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored ./gtapps_mp/gtsrcmaps_mp.py
--- ./gtapps_mp/gtsrcmaps_mp.py (original)
+++ ./gtapps_mp/gtsrcmaps_mp.py (refactored)
@ -83,10 +83,10 @
ref_hdu.writeto(outfile,clobber='yes')if savetemp:
- print "Did not delete the following temporary files:"
- print results
+ print("Did not delete the following temporary files:")
+ print(results)
else:
- print "Deleting temporary files..."
+ print("Deleting temporary files...")
for result in results:
os.remove(result[1])@ -105,9 +105,9 @
#There's an error when you only use one bin so you need to
#make sure and compute more than one bin per job.
while len(energies)/float(jobs) < 3:
- print "Too many jobs ({}), reducing by 1".format(jobs)
+ print("Too many jobs ({}), reducing by 1".format(jobs))
jobs = 1 print "Jobs is now {}".format(jobs)
+ print("Jobs is now {}".format(jobs))
energy_arrays = np.array_split(energies,jobs)
options = {'nxpix': nxpix,
@ -132,9 +132,9 @
SQ = [(array,options) for array in energy_arrays]pool = Pool(processes=jobs)
- print "Spawning {} jobs...".format(jobs)
+ print("Spawning {} jobs...".format(jobs))
results = pool.map(run_gtsrcmaps,SQ)
- print "Combining temporary files..."
+ print("Combining temporary files...")
srcmapssum(results, ref_hdu, outfile, savetmp)def cli():
RefactoringTool: Files that were modified:
RefactoringTool: ./gtapps_mp/gtsrcmaps_mp.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored ./gtapps_mp/gttsmap_mp.py
--- ./gtapps_mp/gttsmap_mp.py (original)
++ ./gtapps_mp/gttsmap_mp.py (refactored)
@ -149,7 +149,7 @
command = ("python %s runLike %s %s"
% (this_arg,subdir, tpl_file))
sys.stdout.write("partition %s: " % subdir)
- print command
print(command)
sys.stdout.flush()
subprocess.call(command.split())@ -291,7 +291,7 @
tsmap.merge_results()
if not savetmp:
- print "Deleting temporary files."
+ print("Deleting temporary files.")
tsmap.remove_tempfiles()RefactoringTool: Files that were modified:
RefactoringTool: ./gtapps_mp/gttsmap_mp.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: No changes to ./gtapps_mp/utils.py
RefactoringTool: Files that need to be modified:
RefactoringTool: ./gtapps_mp/utils.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: No changes to ./build/lib/gtapps_mp/__init__.py
RefactoringTool: Files that need to be modified:
RefactoringTool: ./build/lib/gtapps_mp/__init__.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: No changes to ./build/lib/gtapps_mp/utils.py
RefactoringTool: Files that need to be modified:
RefactoringTool: ./build/lib/gtapps_mp/utils.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored ./build/lib/gtapps_mp/gtdiffrsp_mp.py
--- ./build/lib/gtapps_mp/gtdiffrsp_mp.py (original)
+++ ./build/lib/gtapps_mp/gtdiffrsp_mp.py (refactored)@ -21,7 +21,7 @
name of the created event file which can be combined with other
files and/or deleted later.'''
- print("Starting calculation on interval {} to {}".format(times0,times1))
+ print(("Starting calculation on interval {} to {}".format(times0,times1)))
osfilehandle,outfilename = tempfile.mkstemp(suffix=".fits")
filter['rad'] = "INDEF"
@ -47,7 +47,7 @
diffResps['irfs'] = times[5]
diffResps['chatter'] = 0
diffResps.run(print_command=False)
- print("Completed calculation of interval {} to {}".format(times[0],times[1]))
+ print(("Completed calculation of interval {} to {}".format(times[0],times[1])))
return outfilenamedef eventsum(filenames, Outfile, SaveTemp):
@ -112,7 +112,7 @
pool = Pool(processes=bins)
times = np.array([starts,stops,scfiles,evfiles,srcmdls,irfs])- print("Spawning {} jobs...".format(bins))
+ print(("Spawning {} jobs...".format(bins)))
tempfilenames = pool.map(diffrsp,times.transpose())
print("Combining temporary files...")
eventsum(tempfilenames, OutFile, SaveTemp)
RefactoringTool: Files that were modified:
RefactoringTool: ./build/lib/gtapps_mp/gtdiffrsp_mp.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored ./build/lib/gtapps_mp/gtexpmap_mp.py
--- ./build/lib/gtapps_mp/gtexpmap_mp.py (original)
+++ ./build/lib/gtapps_mp/gtexpmap_mp.py (refactored)@ -18,10 +18,10 @
srcrad and nenergies. This function creates a temporary file for
the output and returns that file's name.'''
- print("Starting calculation of region {},{} to {},{}".format(square0[0][0],
+ print(("Starting calculation of region {},{} to {},{}".format(square0[0][0],
square0[1][0],
square0[0][1],
- square0[1][1]))
+ square0[1][1])))
osfilehandle,outfilename = tempfile.mkstemp(suffix=".fits")
expMap['nlongmin'] = "{:,.0f}".format(float(square0[0][0]))
expMap['nlongmax'] = "{:,.0f}".format(float(square0[0][1]))@ -39,10 +39,10 @
expMap['submap'] = "yes"
expMap['chatter'] = 0
expMap.run(print_command=False)
- print("Completed calculation of region {},{} to {},{}".format(square0[0][0],
+ print(("Completed calculation of region {},{} to {},{}".format(square0[0][0],
square0[1][0],
square0[0][1],
- square0[1][1]))
+ square0[1][1])))
return outfilename@ -97,7 +97,7 @
SQ = [(row, SCFile,EVFile,ExpCube,nlong,nlat,IRF,srcrad,nenergy) for row in pairs]
pool = Pool(processes=bins)
- print("Spawning {} jobs...".format(bins))
+ print(("Spawning {} jobs...".format(bins)))
filenames = pool.map(expmap,SQ)
print("Combining temporary files...")
expsum(filenames, OutFile, SaveTemp)
RefactoringTool: Files that were modified:
RefactoringTool: ./build/lib/gtapps_mp/gtexpmap_mp.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored ./build/lib/gtapps_mp/gtltcube_mp.py
--- ./build/lib/gtapps_mp/gtltcube_mp.py (original)
+++ ./build/lib/gtapps_mp/gtltcube_mp.py (refactored)
@ -22,7 +22,7 @
created ltcube file which can be combined with other files and/or
deleted later.'''- print("Starting calculation on interval {} to {}".format(times0,times1))
+ print(("Starting calculation on interval {} to {}".format(times0,times1)))
if times3 != '':
evfile = tempfile.NamedTemporaryFile(suffix=".fits")
filter['ra']="INDEF" @ -59,7 +59,7 @
expCube['zmax'] = times4
expCube['chatter'] = 0
expCube.run(print_command=True)
- print("Completed calculation on interval {} to {}".format(times0,times1))
+ print(("Completed calculation on interval {} to {}".format(times0,times1)))
return outfilename
@ -141,20 +141,20 @
if EVFile != "":
for interval in zip(starts,stops):
- if verbose: print("Looking at interval",interval[0],"to",interval[1])
+ if verbose: print(("Looking at interval",interval[0],"to",interval[1]))
good_times = False
#grrrr. some bug in pyfits doesn't let me do this the python way...
for gti_i in range(len(gti_data)):
if(not good_times):
- if verbose: print(" Checking gti",gti_data[gti_i]['START'],"to",gti_data[gti_i]['STOP'])
+ if verbose: print((" Checking gti",gti_data[gti_i]['START'],"to",gti_data[gti_i]['STOP']))
gti_starts = interval[0] <= gti_data[gti_i]['START'] <= interval[1]
gti_stops = interval[0] <= gti_data[gti_i]['STOP'] <= interval[1]
- if verbose: print(" Does this gti start inside this interval? ", gti_starts)
- if verbose: print(" Does this gti stop inside this interval? ", gti_stops)
+ if verbose: print((" Does this gti start inside this interval? ", gti_starts))
+ if verbose: print((" Does this gti stop inside this interval? ", gti_stops))
good_times = gti_starts or gti_stops
if verbose: print()- if verbose: print(" Are there good times inside this interval? ", good_times)
+ if verbose: print((" Are there good times inside this interval? ", good_times))
if not good_times:
redo = True
if verbose: print()@ -164,17 +164,17 @
print("No good time intervals found. Bailing...")
sys.exit(1)
print("One (or more) of the slices doesn't have a GTI.")
- print("Reducing the number of threads from ",bins,"to",bins-1)
+ print(("Reducing the number of threads from ",bins,"to",bins-1))
bins -= 1
scfiles = [SCFile for st in scstartssplit]
evfiles = [EVFile for st in scstartssplit]
- print("EVFiles:",evfiles)
+ print(("EVFiles:",evfiles))
zmaxes = [zmax for st in scstartssplit]pool = Pool(processes=bins)
times = np.array([starts,stops,scfiles,evfiles,zmaxes])
- print("Spawning {} jobs...".format(bins))
+ print(("Spawning {} jobs...".format(bins)))
tempfilenames = pool.map(ltcube,times.transpose())
print("Combining temporary files...")
ltsum(tempfilenames, OutFile, SaveTemp)
RefactoringTool: Files that were modified:
RefactoringTool: ./build/lib/gtapps_mp/gtltcube_mp.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored ./build/lib/gtapps_mp/gtsrcmaps_mp.py
--- ./build/lib/gtapps_mp/gtsrcmaps_mp.py (original)
++ ./build/lib/gtapps_mp/gtsrcmaps_mp.py (refactored)
@ -105,9 +105,9 @
#There's an error when you only use one bin so you need to
#make sure and compute more than one bin per job.
while len(energies)/float(jobs) < 3:
- print("Too many jobs ({}), reducing by 1".format(jobs))
print(("Too many jobs ({}), reducing by 1".format(jobs)))
jobs = 1
print("Jobs is now {}".format(jobs))
+ print(("Jobs is now {}".format(jobs)))
energy_arrays = np.array_split(energies,jobs)options = {'nxpix': nxpix,
@ -132,7 +132,7 @
SQ = [(array,options) for array in energy_arrays]pool = Pool(processes=jobs)
- print("Spawning {} jobs...".format(jobs))
+ print(("Spawning {} jobs...".format(jobs)))
results = pool.map(run_gtsrcmaps,SQ)
print("Combining temporary files...")
srcmapssum(results, ref_hdu, outfile, savetmp)
RefactoringTool: Files that were modified:
RefactoringTool: ./build/lib/gtapps_mp/gtsrcmaps_mp.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: No changes to ./build/lib/gtapps_mp/gttsmap_mp.py
RefactoringTool: Files that need to be modified:
RefactoringTool: ./build/lib/gtapps_mp/gttsmap_mp.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: No changes to ./setup.py
RefactoringTool: Files that need to be modified:
RefactoringTool: ./setup.py
(fermi_2.0.8) [root@node0518 gtapps_mp-master]# python setup.py install
running install
running bdist_egg
running egg_info
writing gtapps_mp.egg-info/PKG-INFO
writing dependency_links to gtapps_mp.egg-info/dependency_links.txt
writing entry points to gtapps_mp.egg-info/entry_points.txt
writing top-level names to gtapps_mp.egg-info/top_level.txt
reading manifest file 'gtapps_mp.egg-info/SOURCES.txt'
writing manifest file 'gtapps_mp.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
copying gtapps_mp/gttsmap_mp.py -> build/lib/gtapps_mp
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/gtapps_mp
copying build/lib/gtapps_mp/__init__.py -> build/bdist.linux-x86_64/egg/gtapps_mp
copying build/lib/gtapps_mp/utils.py -> build/bdist.linux-x86_64/egg/gtapps_mp
copying build/lib/gtapps_mp/gtdiffrsp_mp.py.bak -> build/bdist.linux-x86_64/egg/gtapps_mp
copying build/lib/gtapps_mp/gtdiffrsp_mp.py -> build/bdist.linux-x86_64/egg/gtapps_mp
copying build/lib/gtapps_mp/gtexpmap_mp.py.bak -> build/bdist.linux-x86_64/egg/gtapps_mp
copying build/lib/gtapps_mp/gtexpmap_mp.py -> build/bdist.linux-x86_64/egg/gtapps_mp
copying build/lib/gtapps_mp/gtltcube_mp.py.bak -> build/bdist.linux-x86_64/egg/gtapps_mp
copying build/lib/gtapps_mp/gtltcube_mp.py -> build/bdist.linux-x86_64/egg/gtapps_mp
copying build/lib/gtapps_mp/gtsrcmaps_mp.py.bak -> build/bdist.linux-x86_64/egg/gtapps_mp
copying build/lib/gtapps_mp/gtsrcmaps_mp.py -> build/bdist.linux-x86_64/egg/gtapps_mp
copying build/lib/gtapps_mp/gttsmap_mp.py -> build/bdist.linux-x86_64/egg/gtapps_mp
byte-compiling build/bdist.linux-x86_64/egg/gtapps_mp/__init__.py to init.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/gtapps_mp/utils.py to utils.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/gtapps_mp/gtdiffrsp_mp.py to gtdiffrsp_mp.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/gtapps_mp/gtexpmap_mp.py to gtexpmap_mp.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/gtapps_mp/gtltcube_mp.py to gtltcube_mp.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/gtapps_mp/gtsrcmaps_mp.py to gtsrcmaps_mp.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/gtapps_mp/gttsmap_mp.py to gttsmap_mp.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying gtapps_mp.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying gtapps_mp.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying gtapps_mp.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying gtapps_mp.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying gtapps_mp.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating 'dist/gtapps_mp-1.5-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 gtapps_mp-1.5-py3.7.egg
Copying gtapps_mp-1.5-py3.7.egg to /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages
Adding gtapps-mp 1.5 to easy-install.pth file
Installing gtdiffrsp_mp script to /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/bin
Installing gtexpmap_mp script to /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/bin
Installing gtltcube_mp script to /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/bin
Installing gttsmap_mp script to /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/binInstalled /soft/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0/lib/python3.7/site-packages/gtapps_mp-1.5-py3.7.egg
Processing dependencies for gtapps-mp==1.5
Finished processing dependencies for gtapps-mp==1.5
(fermi_2.0.8) [root@node0518 gtapps_mp-master]# popd
/scratch/vanecka/build/sl7/gen5-mic/fermitools/2.0.8_gcc_9.3.0
(fermi_2.0.8) [root@node0518 2.0.8_gcc_9.3.0]# cd $APP_TMP
(fermi_2.0.8) [root@node0518 2.0.8_gcc_9.3.0]# wget https://fermi.gsfc.nasa.gov/ssc/data/analysis/user/SED_scripts_v13.1.tgz O SED_scripts_v13.1.tgz https://fermi.gsfc.nasa.gov/ssc/data/analysis/user/SED_scripts_v13.1.tgz
--2022-05-24 16:11:49-
Connecting to 172.31.1.254:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 721155 (704K) [application/x-tar]
Saving to: ‘SED_scripts_v13.1.tgz’
100%[==================================================================================================================================================================================================================================================================================================================================>] 721,155 131KB/s in 6.7s
2022-05-24 16:11:57 (105 KB/s) - ‘SED_scripts_v13.1.tgz’ saved [721155/721155]
(fermi_2.0.8) [root@node0518 2.0.8_gcc_9.3.0]# wget https://www.slac.stanford.edu/~lott/ABM_mult_P8.tar.gz O ABM_mult_P8.tar.gz https://www.slac.stanford.edu/~lott/ABM_mult_P8.tar.gz
--2022-05-24 16:11:58-
Connecting to 172.31.1.254:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 25945342 (25M) [application/x-gzip]
Saving to: ‘ABM_mult_P8.tar.gz’
69% [===============================================================================================================================================================================================================================> ] 18,071,552 --.-K/s in 6m 24s
2022-05-24 16:18:25 (46.0 KB/s) - Connection closed at byte 18071552. Retrying.
--2022-05-24 16:18:26-- (try: 2) https://www.slac.stanford.edu/~lott/ABM_mult_P8.tar.gz
Connecting to 172.31.1.254:3128... connected.
Proxy request sent, awaiting response... 206 Partial Content
Length: 25945342 (25M), 7873790 (7.5M) remaining [application/x-gzip]
Saving to: ‘ABM_mult_P8.tar.gz’
100%[++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++==================================================================================================>] 25,945,342 222KB/s in 36s
2022-05-24 16:19:03 (215 KB/s) - ‘ABM_mult_P8.tar.gz’ saved [25945342/25945342]
(fermi_2.0.8) [root@node0518 2.0.8_gcc_9.3.0]# cd $CONDA_PKGS_DIRS
(fermi_2.0.8) [root@node0518 site-packages]# tar -xf $APP_TMP/SED_scripts_v13.1.tgz
(fermi_2.0.8) [root@node0518 site-packages]# tar -xf $APP_TMP/ABM_mult_P8.tar.gz
(fermi_2.0.8) [root@node0518 site-packages]# conda deactivate
Run 'mamba init' to be able to run mamba activate/deactivate
and start a new shell session. Or use conda to activate/deactivate.
$ conda deactivate(fermi_2.0.8) [root@node0518 site-packages]# chown $HPC_OWNER:$HPC_GROUP $APP_DEST $(dirname /soft/sl7/gen5-mic/modules/physical-sciences/fermitools/2.0.8_gcc_9.3.0) -R