Commit Graph

221 Commits

Author SHA1 Message Date
kmdunseath cb0b432041 Added file src/msspec/spec/fortran/eig/common/save_eigenvalues.f
which writes the eigenvalues to a fortran stream file called
eigenvalues.dat, facilitating reading by a python script.

Added call to save_eigenvalues in src/msspec/spec/fortran/eig/common/eig_mat_ms.f
2023-06-01 15:52:11 +02:00
Sylvain Tricot 39ba8c3983 Merge tag '1.7.post13' into devel
1.7.post13
2023-03-29 11:45:17 +02:00
Sylvain Tricot c9aa391634 Merge branch 'hotfix/1.7.post13' 2023-03-29 11:45:01 +02:00
Sylvain Tricot cf74431c31 Fix new dtype values for Numpy.
Numpy does not allow anylonger types np.int or np.float.
These are replaced simply by int and float python native types.
2023-03-29 11:41:52 +02:00
Sylvain Tricot f94426476d Add multistage build
To reduce the size of the Docker image. We use a multistage
build based on an alpine distro, the size is reduced by a
factor of 7.
2022-10-27 16:06:51 +02:00
Sylvain Tricot d1e52eae86 Switch to pyprojetc.toml
The packaging uses now the modern pyproject.toml and setup.cfg files.
The setup.py is deprecated.
2022-10-27 14:45:38 +02:00
Sylvain Tricot 6f254e688e Change the version mechanism 2022-10-26 17:15:24 +02:00
Sylvain Tricot 6785e7228a Fix attrdict issue when building wxPython>=4.2.0
When building wxPython, the "attrdict" package is needed, but is
now incompatible with Python > 3.10, due to the "collections" package.
The workaround is to ship a patched version of "attrdict" along with
msspec since "attrdict" isn't developped anylonger.
2022-10-25 16:24:23 +02:00
Sylvain Tricot c455b3bdfa Fix bug with matplotlib > 3.4.3
In newer versions of matplotlib, the autoscale was not working.
Changing "autoscale" to False simply fixes the bug...
2022-10-25 16:21:38 +02:00
Sylvain Tricot bbc8a92382 Merge tag '1.7.post12' into devel
1.7.post12
2022-10-06 18:27:24 +02:00
Sylvain Tricot 0699f193b3 Merge branch 'hotfix/1.7.post12' 2022-10-06 18:24:31 +02:00
Sylvain Tricot 2bdc9943b9 Fix numpy bug with alen()
* The numpy.alen() function is deprecated. We use len() instead
* The use of pkg_resources is discouraged. We use importlib.metadata
  instead. I also removed setuptools_scm get_version. I switch to
  a simple call to "git describe", easier now that we use git flow
* The build fails with python3.10 if compiling wx from sources.
  A fix in the Makefile will be proposed in a future commit.
2022-10-06 18:19:16 +02:00
Sylvain Tricot c0d5e97b35 Merge tag '1.7.post11' into devel
1.7.post11
2022-10-05 13:55:33 +02:00
Sylvain Tricot b6f2531999 Merge branch 'hotfix/1.7.post11' 2022-10-05 13:44:04 +02:00
Sylvain Tricot a4351f5606 Add a "light" installation of msspec
This is similar to a "devel" installation, but only the
virtualenv is created and the msspec package is installed
inside (not in edit mode). Bindings to the Fortran code
are not built.

It is intended to use msspec functions to create clusters but
without having to install wx.
2022-10-05 13:40:22 +02:00
Sylvain Tricot adb73f7fd8 Merge branch 'feature/polarization' into devel
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
2022-02-15 17:30:12 +01:00
Sylvain Tricot 9787e99d2e Added the binding for polarization keyword.
The polarization keyword may be None, 'linear_qOz', 'linear_xOy' or
'circular'. The IPOL parameter in spec.dat is set accordingly to
0, 1, -1 or 2 respectively.
2022-02-15 15:37:28 +01:00
Sylvain Tricot 4b75be2045 Changed 'python' command in sdist target.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
The 'python' command might not be the true interpreter. It is
better to use the provided PYTHON_EXE command.
2022-02-15 15:34:30 +01:00
Sylvain Tricot 25fd8114a5 Merge branch 'feature/correlation_expansion' into devel
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
2022-02-15 11:01:22 +01:00
Sylvain Tricot 39074f75b6 Fixed some minor bugs.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
Fixed some bugs. The correlation expansion version now compiles!
The shared object is imported in the calculator.py module.
2022-02-09 19:08:22 +01:00
Sylvain Tricot 6986dde636 Added main anf Makefile rules for CE. 2022-02-09 19:07:03 +01:00
Sylvain Tricot d09ba1b590 Added main_phd_ns_ce.f
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
This file was updated to be compatible with Python bindings.
The begining of the file is identical to the series expansion
version, so it was copied from there.
2022-02-09 14:35:26 +01:00
Sylvain Tricot f4f204305e Added lapack_axb.f
This file is the same as for the matrix inversion.
2022-02-09 14:34:52 +01:00
Sylvain Tricot 2b6a8b6e05 Added phddif_ce.f file.
The file was updated to be compatible with Python bindings.
2022-02-09 14:19:30 +01:00
Sylvain Tricot 9ebf6c6bc3 Added coumat.f and treat_phd.f
Those 2 files were copied from the phd_se version since
they are identical.
2022-02-09 14:18:22 +01:00
Sylvain Tricot 998fdbee88 Added ms_cor.f file.
The file ms_cor.f was updated to be compatible with Python
bindings.
2022-02-09 13:46:03 +01:00
Sylvain Tricot b1f34aef6a Added mpis.f file.
The file mpis.f was updated to be compatible with Python
bindings. The module CORREXP_MOD was created and is now
allocated in memalloc/allocation.f. The parameter NLMM was
added to dim_mod.f.
2022-02-09 13:39:28 +01:00
Sylvain Tricot 58e9731ffd Added gaunt_st.f file.
The file gaunt_st.f was updated to be compatible with Python
bindings. The module GAUNT_C was created.
2022-02-09 13:24:07 +01:00
Sylvain Tricot 0b889681d1 Added corexp1.f file
The file corexp1.f was updated to be compatible with Python
bindings.
2022-02-09 13:11:17 +01:00
Sylvain Tricot f262f96004 Added and updated corexp.f
The file corexp.f was updated to be compatible with Python
bindings.
2022-02-09 13:08:06 +01:00
Sylvain Tricot e3c0accbcb Added and updated coefpq.f
The file coefpq.f was updated to be compatible with Python
bindings. The common /Q_ARRAY/ was refactored as a module in
memalloc/modules.f and allocated in memalloc/allocation.f.
2022-02-09 12:22:05 +01:00
Sylvain Tricot 39eb3dc9d8 Added and updated cmngr.f
The file cmngr.f was updated to be compatible with Python bindings.
2022-02-09 12:02:24 +01:00
Sylvain Tricot 1dba5cbe47 Added files common to SE and CE.
5 files are common to Series Expansion and Correlation Expansion
algortithms. They are now in the dedicated phd_ce_noso_nosp_nosym
folder.
2022-02-09 11:43:35 +01:00
Sylvain Tricot ca1fd04163 Modified cut_cylinder and cut_plane functions.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
cut_cylinder and cut_plane functions were too slow due to
lists modifications in for loops. Implementation was modified
a bit while keeping the same API.
For now, cutting a cylinder for an axis 'x' or 'y' is not supported
anymore.
2022-02-08 15:20:32 +01:00
Sylvain Tricot a657b1874e Changed memory requirements. 2022-02-08 15:19:26 +01:00
Sylvain Tricot 1fd9509608 Added the malloc keyword.
In the stereo scan, the malloc keyword is now specified.
2022-02-08 14:39:03 +01:00
Sylvain Tricot 74ca8f467f Removed malloc NPH_M parameter.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
In get_theta_phi_scan, the malloc keyword was given
with NPH_M=8000. It was enough for most of calculations
but it was also impossible to change in cases where more
memory was needed. The keyword is now removed so that
it can be direclty specified by the user if needed.
The default value was increased to 8000 instead of 2000.
2021-12-13 18:51:12 +01:00
Sylvain Tricot 38023dcd52 Bug in matplotlib 3.5.0
epsi-builds/msspec_python3/pipeline/head This commit looks good Details
There is presumably a bug when using pcolormesh
with msspec in matplotlib 3.5.0. The stereo projection
does not work properly and the CPU is rising at 100% as
well as the memory usage. Meanwhile, the event loop of Wx
is affected freezing the GUI. Reverting to last stable 3.4.3
version fixes the problem for now. A true fix should be found
asap.
2021-12-02 12:20:40 +01:00
Sylvain Tricot 75c599de95 Added 'other_parameters' keyword in _get_scan.
epsi-builds/msspec_python3/pipeline/head This commit looks good Details
This allows to set or modify any option right before runing
Phagen and Spec. Mostly for debug purposes.
2021-11-30 17:53:47 +01:00
Sylvain Tricot e36373a576 Fixed bug in 'mean_free_path' option.
It was impossible to enter a numerical value.
The 'allowed_values' keyword was set in the definition
of the 'mean_free_path' parameter, I commented it to
allow any value for this option.
2021-11-30 16:56:20 +01:00
Sylvain Tricot 925d694099 Added 'other_parameters' keyword to any scan.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
This keyword is a dictionary allowing any option
to be passed to Phagen or Spec just before runing
the calculation. It is usefull to pass special options
that are for example set automatically otherwise.
2021-11-30 16:26:10 +01:00
Sylvain Tricot 7567b920a1 Add Lapack/Blas compilation flag. 2021-11-30 16:21:05 +01:00
Sylvain Tricot 369e743197 Removed all f-strings.
By replacing f-strings by the standard ".format" call,
the package can be now compatible with python3.5
2021-09-27 17:49:48 +02:00
Sylvain Tricot ec0fc248ce Merge branch 'master' into devel
epsi-builds/msspec_python3/pipeline/head This commit looks good Details
2021-09-27 16:19:24 +02:00
Sylvain Tricot 8269d35420 Updated venv target in Makefile.
epsi-builds/msspec_python3/pipeline/head This commit looks good Details
The 'venv' target has been modified to ensure that
setuptools is at the latest version, otherwise the
docker image could not be created.

Dockerfile was modified to pull the master branch
instead of the devel one.
2021-09-27 15:50:52 +02:00
Sylvain Tricot 0d6db43597 Removed 'syncing website' stage
epsi-builds/msspec_python3/pipeline/head This commit looks good Details
In the CI, the website is not uploaded at the
end of the process for the 'devel' branch.
2021-09-27 14:33:17 +02:00
Sylvain Tricot d6882b57b9 Tried to fix the broken 'syncing website' stage.
epsi-builds/msspec_python3/pipeline/head This commit looks good Details
This last stage is not working due to permission
issues on the server side. I tried to just update
existing files instead of removing everything and
copying new files. Let's see...
2021-09-27 14:17:25 +02:00
Sylvain Tricot e1659db33b Updated the git repo link in 'install section'
The previous link pointed to the devel branch of the repo.
Replaced by the master branch
2021-09-27 14:16:07 +02:00
Sylvain Tricot 89b2a378a5 Fixed bug in copper tutorial.
In the first example lines of the copper tutorial, the line
'view(cluster)' raised an error since the 'cluster' variable
was not yet declared. Replaced by 'view(copper)'.
2021-09-27 14:14:27 +02:00
Sylvain Tricot 4d3ac28343 Added the syncing website section in CI
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
A stage to update the website was added to the
Jenkinsfile.
2021-09-24 17:02:03 +02:00