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msspec_python3
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46 Commits

Author SHA1 Message Date
Sylvain Tricot 3c387c8585 Fix bug in Jenkinsfile 
The "create setup file" failed because coverage module was not found.
It is installed in the virtualenv so the command load the venv first now.
 2019-12-06 13:49:28 +01:00
Sylvain Tricot c5187e3c4b Fix bug in Jenkinsfile. 
The PYTHONPATH variable is passed in the stage steps to tell Python where
to find the msspec package.
 2019-12-06 13:43:31 +01:00
Sylvain Tricot c22f86fe76 Fix bug in install process. 
The *.so are now in the fortran folders, so the MANIFEST.in file was updated
to include those shared objects in the pip source distribution
 2019-12-06 13:26:22 +01:00
Sylvain Tricot 93782236b0 Add the eigen value "spectroscopy" support. 
The msspec/spec/fortran folder is totally different now. Most of the
fortran subroutines are in their own file and are located in different folders

The Makefile has been rewritten and can generate 3 libraries:
- one for Photoelectron Diffration in series expansion
- two for Eigen value calculation with matrix inversion and power method
 2019-12-05 18:26:41 +01:00
Sylvain Tricot 47adb16ccc coverage moved to results target in src/Makefile 2019-11-29 18:06:59 +01:00
Sylvain Tricot 047458dcf6 Add test coverage report in documentation 
Now tests are run through the coverage utility and a report is generated
and available in the FAQ of the html doc.
 2019-11-29 17:38:41 +01:00
Sylvain Tricot bdd3c7c941 Fix bug in documentation configuration 
sys.path was updated to fit the new file hirerarchy (one '../' removed)
 2019-11-29 15:45:55 +01:00
Sylvain Tricot b698eb7cfe Fix bug in install script for the gfortran version 
add "|cut -d. -f1" to keep only the major version number
 2019-11-29 15:33:45 +01:00
Sylvain Tricot 9296509f7b Work on installation script. 
Change gfortran min version to 6.0 to see if this works in Jenkins
 2019-11-29 15:27:14 +01:00
Sylvain Tricot 56c1031e36 Work on CI 
Fix the bug in load .profile (changed to ~/.profile)...
 2019-11-29 14:26:13 +01:00
Sylvain Tricot 28e9065d29 Work on CI 
Load the .profile user's file for the make selfex stage since the path
to makeself is not standard
 2019-11-29 14:23:03 +01:00
Sylvain Tricot dcda10d1b5 Improve Python < 3.6 compatibility. 
f-strings are removed as it is only available since Python >=3.6
 2019-11-29 14:04:41 +01:00
Sylvain Tricot 54b7e409a0 Work on continuous integration 
Add VERBOSE=1 in the make calls in the Jenkinsfile to help debugging
the build jobs in Jenkins
 2019-11-29 13:47:52 +01:00
Sylvain Tricot fb671a065e Work on continuous integration. 
Changes in the main Makefile to include a "venv" and a "doc" targets
The Jenkinsfile now uses only the Makefile. The CI/CI.bash shell script
should not bu used anymore and will be deleted in a future commit.
 2019-11-29 13:20:40 +01:00
Sylvain Tricot 9d76465b11 Resolve install.sh confict with previous commit 2019-11-28 18:44:39 +01:00
Sylvain Tricot ad52398853 Merge branch 'master' of https://git.ipr.univ-rennes1.fr/epsi/msspec_python3 2019-11-28 18:43:33 +01:00
Sylvain Tricot 4eceb1bf26 Simplify the install process. 
The installation script does not try anymore to create a virtual environment.
A message at the begining recommends to the user to be in a virtual env. That way
it is possible to use virtualenv, conda, python - m venv or none of this to
create (or not) a virtual environment. It's up to the user.

The script is simpler and *should* be POSIX compliant

Files that have been modified in this commit:
- Makefile
- src/Makefile
- src/msspec/spec/fortran/Makefile
- src/msspec/phagen/fortran/Makefile
- src/install.sh
 2019-11-28 18:35:37 +01:00
Kevin Dunseath 1e67616733 Changes to src/install.sh to allow installation under Mac OSX 
In phagen_scf.f, subroutine atom_sub: changed dimensions of r_hs, rho0_hs to be assumed size arrays
 2019-11-27 16:03:49 +01:00
Sylvain Tricot 4a5f6f1161 Add Renormalization option in the python interface 2019-11-27 14:09:55 +01:00
Sylvain Tricot 13a43b0b70 Fix bug in memory management 
the call to the run function in libspec cannot be done
with unzip the OrderedDict values. It creates memory address
confusion and the program is killed by the os with a message:
"Operating system error: Cannot allocate memory
 Allocation would exceed memory limit"

To fix, we shall call the run function with each argument well specified
between the parentheses.
 2019-11-22 13:38:28 +01:00
Sylvain Tricot a28570974e Add the doc folder with all *.rst files 
This is used to create the pdf manual and html website
 2019-11-22 11:39:39 +01:00
Sylvain Tricot 59c43395c2 Work on install script 2019-11-21 17:09:19 +01:00
Sylvain Tricot 4807474889 Work on continuous integration 
* Started port of the previous CI.bash
* Also fix bug in spec.f (stdout was closed so nothing appeared on screen
  at the second call to libspec)
* Work on test suite
  - utils to create clusters are tested
  - PED calculator for polar and azimutal scans are tested
 2019-11-20 18:14:00 +01:00
Sylvain Tricot d167bd9f75 Add a help message for options in install.sh 2019-11-19 14:07:57 +01:00
Sylvain Tricot a1fe98b7a3 Add a Jenkinsfile for continuous integration 2019-11-19 13:20:48 +01:00
Sylvain Tricot 42a327501e Work on install script 
Add support for user local install
Add support for already existing venv
 2019-11-19 00:38:08 +01:00
Sylvain Tricot 51afffd97b Work on install script 2019-11-18 17:33:32 +01:00
Sylvain Tricot 9222f5c9d2 Fix bug in install target 2019-11-18 00:37:34 +01:00
Sylvain Tricot 9c4b3320e4 Change Makefile "selfex" target 2019-11-17 23:28:53 +01:00
Sylvain Tricot 3f2659780c Work on package creation. 2019-11-17 23:27:10 +01:00
Sylvain Tricot a3469c53df work on packaging 2019-11-16 00:38:17 +01:00
Sylvain Tricot 960a954e02 Work on CI 2019-11-15 16:54:08 +01:00
Sylvain Tricot d280d782ff Add .gitattributes 2019-11-15 16:53:41 +01:00
Sylvain Tricot 45034a44cd Update version 2019-11-15 16:51:07 +01:00
Sylvain Tricot ba80b3c88d work on CI set_version 2019-11-15 16:48:05 +01:00
Sylvain Tricot 189f60e1d8 iUpdate the license info 2019-11-15 16:24:12 +01:00
Sylvain Tricot 500d822c11 change bug in hooks/pre-commit 2019-11-15 16:15:15 +01:00
Sylvain Tricot 56163bacbe Update README info 2019-11-15 16:13:02 +01:00
Sylvain Tricot 923f5580e8 Add version target in toplevel Makefile 2019-11-15 16:07:48 +01:00
Sylvain Tricot 85cc7d788a test hook again 2019-11-15 15:56:02 +01:00
Sylvain Tricot bfe74ecbc4 Add VERSION file 2019-11-15 15:31:29 +01:00
Sylvain Tricot 4e6316b567 test pre-commit hook 2019-11-15 15:27:33 +01:00
Sylvain Tricot c0ad93cea0 Add update_version.py and CI folder 2019-11-15 14:26:16 +01:00
Sylvain Tricot eee2516a02 Add new file hierarchy 2019-11-15 11:16:06 +01:00
Sylvain Tricot bb3a861ba2 Reorganize file hierarchy 
Add Makefiles to create setup file
 2019-11-15 11:13:33 +01:00
Sylvain Tricot ef5be70e4c Initial commit for the dynamic version 2019-11-14 15:16:51 +01:00