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pycrysfml v0.1.0 #13

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Jul 24, 2024
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824dc8e
Try new implementation of pycfml
AndrewSazonov Jul 10, 2024
eb8227f
Add CFML_Utilities module
AndrewSazonov Jul 10, 2024
8b760ab
Add building pycfml so
AndrewSazonov Jul 11, 2024
048701e
Some debugging
AndrewSazonov Jul 11, 2024
7fd4e4f
Add missing CFML_Wraps_Utils
AndrewSazonov Jul 11, 2024
3f26973
Clean up
AndrewSazonov Jul 11, 2024
86e1c6c
Trigger new backend
AndrewSazonov Jul 11, 2024
6ed2852
Add missing Wraps_Atoms
AndrewSazonov Jul 11, 2024
c3111a9
Add 'Download PYCFML repository' step
AndrewSazonov Jul 11, 2024
a3a2e37
Temporarily keep only ubuntu-22.04 + ifort
AndrewSazonov Jul 11, 2024
120c10d
More dedug
AndrewSazonov Jul 11, 2024
2d34807
Update unit tests to follow new api syntax
AndrewSazonov Jul 11, 2024
d584ef8
Add py api files to pycfml dist
AndrewSazonov Jul 11, 2024
2f33641
Restructure CI script
AndrewSazonov Jul 11, 2024
f285763
Switch to the new structure of CrysFML2008
AndrewSazonov Jul 11, 2024
f6bf18a
debug pycfml unit tests
AndrewSazonov Jul 11, 2024
fdaf440
Add change_runpath_for_built_pycfml
AndrewSazonov Jul 11, 2024
0b637e8
debug
AndrewSazonov Jul 11, 2024
a355d65
Debug pycfml import
AndrewSazonov Jul 12, 2024
0e4ff52
More debug
AndrewSazonov Jul 12, 2024
dee2dde
More debug
AndrewSazonov Jul 12, 2024
08ab361
Try windows CI
AndrewSazonov Jul 12, 2024
8203351
Temporarily disable parallel builds
AndrewSazonov Jul 12, 2024
013d80d
Try link *.obj
AndrewSazonov Jul 12, 2024
3b0bd02
New template for building pycfml shared object
AndrewSazonov Jul 12, 2024
15804cd
Add 'Math_In_Limits' to the CrysFML build
AndrewSazonov Jul 12, 2024
f4c3614
add macos and clean up
AndrewSazonov Jul 12, 2024
fb77b94
Temporarily disable macos CI
AndrewSazonov Jul 12, 2024
a0b9b28
Clean up
AndrewSazonov Jul 12, 2024
1edf283
Add missing CFML modules
AndrewSazonov Jul 12, 2024
85c3a16
Disable some problematic modules
AndrewSazonov Jul 12, 2024
f59019d
Refactor build scripts
AndrewSazonov Jul 15, 2024
f572a7d
rename package from pyproject08 to pyproject
AndrewSazonov Jul 15, 2024
27b3055
add change_runpath_for_built_pycfml
AndrewSazonov Jul 15, 2024
9bf35f7
Refactoring
AndrewSazonov Jul 15, 2024
cbc8a39
Rename pycrysfml08 to pycrysfml in tests
AndrewSazonov Jul 15, 2024
d03cfd3
Add build CFML test programs
AndrewSazonov Jul 15, 2024
ef7c7d4
Add run CFML test programs
AndrewSazonov Jul 15, 2024
7b45cff
Fix CFML functional tests
AndrewSazonov Jul 16, 2024
a3b42db
debug
AndrewSazonov Jul 16, 2024
2fb0423
Capitalize test dirs
AndrewSazonov Jul 16, 2024
cb91d57
Clean up
AndrewSazonov Jul 16, 2024
dff71a9
Follow update in CrysFML2008
AndrewSazonov Jul 17, 2024
2f2069c
Update PythonAPI folder name
AndrewSazonov Jul 17, 2024
e64c4e5
Try uv to install python deps
AndrewSazonov Jul 17, 2024
758cd40
Remove uv
AndrewSazonov Jul 17, 2024
e3e4ed9
Colorize terminal output
AndrewSazonov Jul 17, 2024
3c5a493
Update scripts.py
AndrewSazonov Jul 17, 2024
11b84f3
fix colors
AndrewSazonov Jul 17, 2024
312b32a
Debug color
AndrewSazonov Jul 19, 2024
52c2330
Add flag to enable backslash escapes
AndrewSazonov Jul 19, 2024
54a87f9
Add all platforms
AndrewSazonov Jul 19, 2024
461de7f
Try on ubuntu only
AndrewSazonov Jul 19, 2024
8db0946
Fix build pycfml lib cmd
AndrewSazonov Jul 19, 2024
245c86e
Try ubuntu only
AndrewSazonov Jul 19, 2024
d3609ac
Change build pycfml cmd back
AndrewSazonov Jul 19, 2024
e8f5193
Enable all platforms
AndrewSazonov Jul 19, 2024
f6f2699
Add Wraps_Utilities.f90
AndrewSazonov Jul 20, 2024
4a4ae1a
emporary disable due to error when building pycfml shared object
AndrewSazonov Jul 20, 2024
8f1185c
Try calculating diffraction pattern
AndrewSazonov Jul 21, 2024
13cec27
Fix macos rpath change script
AndrewSazonov Jul 22, 2024
f46aaa2
Add more debug
AndrewSazonov Jul 22, 2024
1504cca
Update pycfml import debug
AndrewSazonov Jul 22, 2024
a3dbc8f
Try macos 12 + ifort build combination
AndrewSazonov Jul 22, 2024
299fb04
Modify __init__.py
AndrewSazonov Jul 22, 2024
13e8403
Suppress the error message when copying files
AndrewSazonov Jul 22, 2024
d9238c4
Enable macos-12 + ifort
AndrewSazonov Jul 22, 2024
1c421e8
Fix suppress the error message command
AndrewSazonov Jul 22, 2024
b54570c
Add pycrysfml unit tests
AndrewSazonov Jul 22, 2024
5a65e76
Allow parallel builds
AndrewSazonov Jul 22, 2024
26c6e32
Fix python wheel name on macos
AndrewSazonov Jul 22, 2024
c041506
Add examples, issues, extend tests
AndrewSazonov Jul 23, 2024
a7af488
Fix python package name on macos
AndrewSazonov Jul 23, 2024
26e4f7a
Fix powder pattern from json tests
AndrewSazonov Jul 23, 2024
9ee6a3d
Update examples and issues
AndrewSazonov Jul 23, 2024
59f2075
Licensing (#11)
AndrewSazonov Jul 23, 2024
da7b791
Update project description
AndrewSazonov Jul 23, 2024
c5486b9
Upload python wheel to GH releases
AndrewSazonov Jul 23, 2024
b981b79
Add new step to publish python wheels
AndrewSazonov Jul 23, 2024
2902880
Fix required python version to be >= 3.9
AndrewSazonov Jul 23, 2024
60bc8f1
Add CI build on pull_request
AndrewSazonov Jul 23, 2024
a581c55
Switch from tomllib to toml to support python <3.11
AndrewSazonov Jul 23, 2024
5b819ee
Add missing toml lib
AndrewSazonov Jul 23, 2024
23643bb
Remove python 3.9 from build matrix
AndrewSazonov Jul 23, 2024
744557c
Minor fixes
AndrewSazonov Jul 23, 2024
a463ba6
Do not suppress error messages
AndrewSazonov Jul 23, 2024
760b73e
Update rpath delete template to follow gcc bump from 13.2.0 to 13.3.0
AndrewSazonov Jul 23, 2024
9b94507
Clean up
AndrewSazonov Jul 23, 2024
c1c69df
Fix rpaths
AndrewSazonov Jul 24, 2024
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318 changes: 256 additions & 62 deletions .github/workflows/main.yml

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13 changes: 11 additions & 2 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,20 @@ __pycache__
build
*.spec

# PyCharm
.idea

# macOS
.DS_Store

# Misc
# Build
.venv
.benchmarks/local
crysfml*
pycrysfml*
build
dist
repo
scripts

# Misc
.benchmarks/local
674 changes: 674 additions & 0 deletions COPYING

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165 changes: 165 additions & 0 deletions COPYING.lesser
Original file line number Diff line number Diff line change
@@ -0,0 +1,165 @@
GNU LESSER GENERAL PUBLIC LICENSE
Version 3, 29 June 2007

Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.


This version of the GNU Lesser General Public License incorporates
the terms and conditions of version 3 of the GNU General Public
License, supplemented by the additional permissions listed below.

0. Additional Definitions.

As used herein, "this License" refers to version 3 of the GNU Lesser
General Public License, and the "GNU GPL" refers to version 3 of the GNU
General Public License.

"The Library" refers to a covered work governed by this License,
other than an Application or a Combined Work as defined below.

An "Application" is any work that makes use of an interface provided
by the Library, but which is not otherwise based on the Library.
Defining a subclass of a class defined by the Library is deemed a mode
of using an interface provided by the Library.

A "Combined Work" is a work produced by combining or linking an
Application with the Library. The particular version of the Library
with which the Combined Work was made is also called the "Linked
Version".

The "Minimal Corresponding Source" for a Combined Work means the
Corresponding Source for the Combined Work, excluding any source code
for portions of the Combined Work that, considered in isolation, are
based on the Application, and not on the Linked Version.

The "Corresponding Application Code" for a Combined Work means the
object code and/or source code for the Application, including any data
and utility programs needed for reproducing the Combined Work from the
Application, but excluding the System Libraries of the Combined Work.

1. Exception to Section 3 of the GNU GPL.

You may convey a covered work under sections 3 and 4 of this License
without being bound by section 3 of the GNU GPL.

2. Conveying Modified Versions.

If you modify a copy of the Library, and, in your modifications, a
facility refers to a function or data to be supplied by an Application
that uses the facility (other than as an argument passed when the
facility is invoked), then you may convey a copy of the modified
version:

a) under this License, provided that you make a good faith effort to
ensure that, in the event an Application does not supply the
function or data, the facility still operates, and performs
whatever part of its purpose remains meaningful, or

b) under the GNU GPL, with none of the additional permissions of
this License applicable to that copy.

3. Object Code Incorporating Material from Library Header Files.

The object code form of an Application may incorporate material from
a header file that is part of the Library. You may convey such object
code under terms of your choice, provided that, if the incorporated
material is not limited to numerical parameters, data structure
layouts and accessors, or small macros, inline functions and templates
(ten or fewer lines in length), you do both of the following:

a) Give prominent notice with each copy of the object code that the
Library is used in it and that the Library and its use are
covered by this License.

b) Accompany the object code with a copy of the GNU GPL and this license
document.

4. Combined Works.

You may convey a Combined Work under terms of your choice that,
taken together, effectively do not restrict modification of the
portions of the Library contained in the Combined Work and reverse
engineering for debugging such modifications, if you also do each of
the following:

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document.

c) For a Combined Work that displays copyright notices during
execution, include the copyright notice for the Library among
these notices, as well as a reference directing the user to the
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for conveying Corresponding Source.)

5. Combined Libraries.

You may place library facilities that are a work based on the
Library side by side in a single library together with other library
facilities that are not Applications and are not covered by this
License, and convey such a combined library under terms of your
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on the Library, uncombined with any other library facilities,
conveyed under the terms of this License.

b) Give prominent notice with the combined library that part of it
is a work based on the Library, and explaining where to find the
accompanying uncombined form of the same work.

6. Revised Versions of the GNU Lesser General Public License.

The Free Software Foundation may publish revised and/or new versions
of the GNU Lesser General Public License from time to time. Such new
versions will be similar in spirit to the present version, but may
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41 changes: 25 additions & 16 deletions LICENSE
Original file line number Diff line number Diff line change
@@ -1,19 +1,28 @@
Copyright (c) 2018 The Python Packaging Authority
----------------------------------------------------
Crystallographic Fortran Modules Library (CrysFML08)
----------------------------------------------------

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The CrysFML08 project is distributed under LGPL. In agreement with the
Intergovernmental Convention of the ILL, this software cannot be used
in military applications.

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
Copyright (C) 2019-2020 Institut Laue-Langevin (ILL), Grenoble, FRANCE
Universidad de La Laguna (ULL), Tenerife, SPAIN
Laboratoire Leon Brillouin(LLB), Saclay, FRANCE

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Authors: Juan Rodriguez-Carvajal (ILL)
Javier Gonzalez-Platas (ULL)
Nebil Ayape Katcho (ILL)

This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 3.0 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public
License along with this library; if not, see <http://www.gnu.org/licenses/>.
21 changes: 10 additions & 11 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,12 @@ This is a repository for testing the build process of both the fortran crystallo

### Build matrix

| Platform / Compiler | gfortran | ifx | ifort | nagfor |
| ------------------------- | -------- | ---------- | ------------- | ---------- |
| Windows 10 | ✅ | ✅ | ✅ | |
| Ubuntu 22.04 | ✅ | ✅ | ✅ | |
| macOS 12 (Intel) | ✅ | Unsupported | ✅ | |
| macOS 14 (Apple Silicone) | ✅ | Unsupported | Unsupported | ✅ Local |
| Platform / Compiler | gfortran | ifx | ifort | nagfor |
| ------------------------- | -------- | ----------- | ------------- | ---------- |
| Windows 10 | ✅ | ✅ | ✅ | |
| Ubuntu 22.04 | ✅ | ✅ | ✅ | |
| macOS 12 (Intel) | ✅ | Unsupported | ✅ | |
| macOS 14 (Apple Silicone) | ✅ | Unsupported | Unsupported | ✅ Local |

### Main steps

Expand All @@ -26,19 +26,19 @@ More details are in the [CI script](.github/workflows/main.yml).

### To run locally

* Create and activate a python environment (_optional_)
* Create and activate a python environment (_optional_)

```
$ python3.11 -m venv .venv
$ source .venv/bin/activate
$ source .venv/bin/activate
```

* Upgrade the package installer for Python (_optional_)

```
$ python -m pip install --upgrade pip
```

* Install Python dependences, including extras

```
Expand All @@ -48,7 +48,7 @@ More details are in the [CI script](.github/workflows/main.yml).
* Print possible options for creating job scripts (_optional_)

```
$ python scripts.py --help
$ python scripts.py --help
```

* Create job scripts with default options
Expand All @@ -68,4 +68,3 @@ More details are in the [CI script](.github/workflows/main.yml).
```
$ scripts/main_script.sh
```

5 changes: 5 additions & 0 deletions RELEASE.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
This is the first release of the pycrysfml python library based on the new auto-generated Python API for CrysFML08 from https://code.ill.fr/scientific-software/CrysFML2008.

### Features

- Simulation of the powder diffraction pattern is implemented in `cfml_utilities`.
12 changes: 12 additions & 0 deletions __init__.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
import os
import sys
import importlib.metadata

# Set package version
__version__ = importlib.metadata.version("pycrysfml")

# Add current path to system path
sys.path.append(os.path.dirname(__file__))

# Set environment variable CRYSFML_DB to be the path to the Databases directory
os.environ['CRYSFML_DB'] = os.path.join(os.path.dirname(__file__), 'Databases')
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