New spack packages for the spack-repo

.github/spack-config/spack.yaml

@@ -6,7 +6,13 @@ spack:
     - py-extra-geom
     - py-karabo-bridge
     - py-msgpack-numpy
-    # - py-pyfai
+    - py-pyfai
     - py-pyopengl
+    - py-dials-data
+    # - py-extra-foam
+    - py-numexpr
+    - py-procrunner
+    - py-silx
+    - py-transformations
   view: False
   concretization: together

packages/py-dials-data/package.py

@@ -0,0 +1,70 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+# ----------------------------------------------------------------------------
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
+#
+# This is a template package file for Spack.  We've put "FIXME"
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
+#
+#     spack install py-dials-data
+#
+# You can edit this file again by typing:
+#
+#     spack edit py-dials-data
+#
+# See the Spack documentation for more information on packaging.
+# ----------------------------------------------------------------------------
+
+from spack import *
+
+
+class PyDialsData(PythonPackage):
+    """A python package providing data files used for regression tests in DIALS, dxtbx, xia2 
+    and related packages.If you want to know more about what py-dials-data is you can have a read 
+    through the background information. For everything else the main documentation is probably 
+    the best start."""
+
+    # FIXME: Add a proper url for your package's homepage here.
+    homepage = "https://dials-data.readthedocs.io/en/latest/"
+    url      = "https://github.com/dials/data/archive/v2.1.0.tar.gz"
+
+    # FIXME: Add a list of GitHub accounts to
+    # notify when the package is updated.
+    maintainers = ['RobertRosca', 'julianhoersch']
+
+    version('2.1.0', sha256='17935ff9e3791dae992f4b606899d407ea8ede7ea047faa6580a7552429c0a7b')
+    version('2.0.0', sha256='d68708af31e6325de30c6f191c05c5299b3a19fba5c657262b8d75fb24af3593')
+    version('1.0.0', sha256='0c28046f95fd89f55ce270eade4bece0862c8aa31c1b3baff3da4a6aa277cadb')
+    version('0.6.0', sha256='84397fa24a6d805f9a223becb4c986e47fa11b2e0abb5373be56aeabe6f28883')
+    version('0.5.0', sha256='317c6bea2db078c342c85845363ccf1487dd8e9178afa33dc3aa034490a23246')
+    version('0.4.0', sha256='35652e5cfa5d49f3b4de0bbdb1067914b788672bbc67c2ec169d982b69e84155')
+    version('0.3.0', sha256='b90480ad6540c05e4017f3e7c1fed43c26f0928e3301e65114b8d5d13d94f50e')
+    version('0.2.0', sha256='8285b619cf56acb50163f2040e5d26c6ea2a7de9606f0d8e9d313977fbbc95f0')
+    version('0.1.0', sha256='5239f50ed13ead45229488bf578806289e5ee5b482d6cbd3a365cd60387aa4e2')
+
+    # FIXME: Add dependencies if required. Only add the python dependency
+    # if you need specific versions. A generic python dependency is
+    # added implicity by the PythonPackage class.
+    depends_on('[email protected]:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('[email protected]:')
+    depends_on('[email protected]') # in install_requires
+    depends_on('[email protected]')
+    depends_on('[email protected]')
+
+    #test dependencies
+    depends_on('py-coverage@:4.9', type='test')
+    # depends_on('py-pytest', type='test') #specify for test too?
+    depends_on('py-pytest-cov', type='test')
+    depends_on('py-testpath', type='test')
+
+    def build_args(self, spec, prefix):
+        # FIXME: Add arguments other than --prefix
+        # FIXME: If not needed delete this function
+        args = []
+        return args

packages/py-dials/package.py

@@ -0,0 +1,126 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+# ----------------------------------------------------------------------------
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
+#
+# This is a template package file for Spack.  We've put "FIXME"
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
+#
+#     spack install py-dials
+#
+# You can edit this file again by typing:
+#
+#     spack edit py-dials
+#
+# See the Spack documentation for more information on packaging.
+# ----------------------------------------------------------------------------
+
+from spack import *
+
+
+class PyDials(PythonPackage):
+    """X-ray crystallography for structural biology has benefited greatly from 
+    a number of advances in recent years including high performance pixel array 
+    detectors, new beamlines capable of delivering micron and sub-micron focus 
+    and new light sources such as XFELs. The DIALS project is a collaborative 
+    endeavour to develop new diffraction integration software to meet the data 
+    analysis requirements presented by these recent advances. There are three end 
+    goals: to develop an extensible framework for the development of algorithms to 
+    analyse X-ray diffraction data; the implementation of algorithms within this 
+    framework and finally a set of user facing tools using these algorithms to 
+    allow integration of data from diffraction experiments on synchrotron and 
+    free electron sources."""
+
+    # FIXME: Add a proper url for your package's homepage here.
+    homepage = "https://dials.github.io"
+    url      = "https://github.com/dials/dials/archive/v3.2.3.tar.gz"
+
+    # FIXME: Add a list of GitHub accounts to
+    # notify when the package is updated.
+    maintainers = ['RobertRosca', 'julianhoersch']
+
+    version('3.3.0',                sha256='163ffd5da4b6c783e5e37ffedae751b86b26d0266c88b95280d727a69180e14c')
+    version('3.2.3',                sha256='e9b52b9bc61595579401bbae2447d42e49a4a30d15c2908bea0899216cf8fedb')
+    version('3.2.2',                sha256='3df1c0d0145d59f176fe81f0e8b23ea28955781021183d2497c183a26ec0a7bb')
+    version('3.2.1',                sha256='1bca865ebb2fa3b8e789dcc1805956934332af7629642c5d556bc6c11bc6583e')
+    version('3.2.0',                sha256='0cd2a8905ee239d8577b2150d9d97d2d83527b26f9d01ce7cb940bd04bd6c3eb')
+    version('3-1-4',                sha256='c54e8948e06ddab5be99e0a499f5f9067d72af97cbaddf9f5d88919fe7aa08ac')
+    version('3-1-3',                sha256='b26aea14ad48fa44a8c1db8fe5ef533e95a1f7ad9b6a2e0048810255fec12709')
+    version('3-1-2',                sha256='47625e40d2dcee5364fa5ba0b2b2256e3f0f58c706179d66cd03acf901ee8181')
+    version('3-1-1',                sha256='68c96a82e8e21b0e5e1dbc85ca00aa4bba91690d9d9a2aee757da00cad4ff636')
+    version('3.1.0',                sha256='031d6073f9c4a40f73e31cd4bb4e466b04a994a47923bea9e7b85b092a687f74')
+    version('3-0-4',                sha256='7c8123868e5d9d8090cc946f694be51b474de92def1876c9a3d468ef71c2ea38')
+    version('3-0-3',                sha256='55b2be86f3079f8d153331c78e2efd88a26471b2a8a134738b1b65be3e86ca06')
+    version('3-0-2',                sha256='dd3be99a91111169bcf0a763f46c86b4352c0e68b3063f7202fc2ef1393cd143')
+    version('3-0-1',                sha256='cdfad52648399e781c02ee8d9d557555a1e99090ebe149b9a953f8bcac8d35ec')
+    version('3.0.0',                sha256='ab39ea80d5e35883087ef36d5b871893fbf8956ee34a22775f6b4e27fb1eb5c2')
+    version('3.dev',                sha256='ccbdf49f0a53d92bffa6e0c463a8d8e438d474d470447809baf2f2d771dd8151')
+    version('2-2-10-macosx-conda3', sha256='32e4e418cf837514eb79c7462073dd8a2605c71299a52e370d00dc6c4c6a98d9')
+    version('2-2-10',               sha256='09468f2fa8abb273e9c34d51bb657a05bf40e472ef668d886b8b21bd54b8af96')
+    version('2-2-9-macosx-conda3',  sha256='48b7fc4c18b59b0bbd7431cb9836f81479d8dd1fbf266f46225f2058faaccf31')
+    version('2-2-9',                sha256='70b615f9f8a152f603d8f65280be3c72c8ea6916e6cba81bc033aff7c2fda450')
+    version('2-2-8-macosx-conda3',  sha256='54250bbc8ecbe37ffef048a4bbb501fab7adcebc0a8b71238c2bf25de486ef67')
+    version('2-2-8',                sha256='8ad6572faf1bd07e2a1aee417c148b9b40c1b04b0356fc2df2ce2bc70368e675')
+    version('2-2-7-macosx-conda3',  sha256='07b9855dffc59aa26ed6d4d842b8338da336b1f732379ca755d6b58e09799bc0')
+    version('2-2-7',                sha256='d22c75eed5198fb9c3e11b0d957590e5caaf404dedc1910b67f6d7cfe47b530a')
+    version('2-2-6-macosx-conda3',  sha256='9ac227d8ddf6117215b4a446118efa2068438d17b8a29abda7d392dcb13014ac')
+    version('2-2-6',                sha256='371ddbee804cfea3e82767919458d0e92c6d7a06227914cc75c9b53034f3df65')
+    version('2-2-5-macosx-conda3',  sha256='234771cb45ea3df336313c2e388909bd522cd17d067501dcb6c872f872b1d8bd')
+    version('2-2-5',                sha256='52301ea90059911cafc9b508f665c279a45fcf0e1945e25e3bf2c7e3be18a0e5')
+    version('2-2-4-macosx-conda3',  sha256='d32ca2719fdf3a546166c916ce638cf7c2a642ca64b42cf0fd204274b1396987')
+    version('2-2-4',                sha256='6007ad8c7912d662ccca2bfc4042ad6914e384e0cc082a9d30b17482f2c7384c')
+    version('2-2-3-macosx-conda3',  sha256='51dea8c04e3bcfae184124da3b63a32e85893d76de2b7fe11f0edd2b2bc79278')
+    version('2-2-3',                sha256='c6428fb633886be0fe27f4c88640c560c259fbb836dd468e79911f124b8fdb31')
+    version('2-2-2-macosx-conda3',  sha256='d9b749642ffd79bb7b7f116e2e2e2511dd627609356ad695500287a6b2ee2bae')
+    version('2-2-2',                sha256='fc7af3b57c9d1ef72eeb9d6d7537dad07de9ca1e7a2e6f713f5707227d8557f8')
+    version('2-2-1-macosx-conda3',  sha256='727a1a5994d806d67e8cf0a788cc0577045a12d5c473512fe0d8557aaaeb9e8a')
+    version('2-2-1',                sha256='f836216fd3aff7e341e045935acbbbc1446a005c0b88cd133cae940941dc566f')
+    version('2-2-0-macosx-conda3',  sha256='3690c19b0ac1d9ad1ffd6e89ee1cf998a4bc38315c5bf3d79a62cf11685a041d')
+    version('2.2.0',                sha256='5b5d8b8bd071f519ac031a2aa8e01819a355ff0647753ac3e30028f05331dce0')
+    version('2-1-5-macosx-conda3',  sha256='f874ee1f0fa35e213fcb7c329c3e642712f5d96dc9c35c7337ade8ddcec49d68')
+    version('2-1-5',                sha256='2744cc7842296913bd6e2794704fd6ba416df0cf4784101f3341386ac0b3b426')
+    version('2-1-4-macosx-conda3',  sha256='e8d4cb4efc48e1fff1e8325c37cfecba525a38ceae75c1254d49d73b8f38b9fe')
+    version('2-1-4',                sha256='7cc48986e6b17a979ac7e8b4d99a03fe8a5d0943f22f437731538ab0802ed6f6')
+    version('2-1-3-macosx-conda3',  sha256='7b5c374643183773f0324971fedc251e9c2db62cf9efdb9c73ee5de09ee79558')
+    version('2-1-3',                sha256='0b35f0c8409edc6f84adc37212a1749fae9ec4cc67b6e1f53a1a4fc8fc8c02d8')
+    version('2-1-2-macosx-conda3',  sha256='e797efd61a95526ea19c92ed896801774f81eb571a03c7f510d7c9e227de588e')
+    version('2-1-2',                sha256='2b5e63419377a14f3d7f17a56eb84f9551fab4eb2568ce0c342a1ba307e0337d')
+    version('2-1-1-macosx-conda3',  sha256='6b436e8cb1c88a8b6226e9511b8c9176e72ac9cfad548537ebbedb1d863f04a8')
+    version('2-1-1',                sha256='c41bb0376d80d60c608778ca0364170369b138f40de37e1823c886b5476373a1')
+    version('2-1-0-macosx-conda3',  sha256='cfce998484e07d9eeec7c645f49f5761a7b1dff871917b7dda60fc1e69e2ba25')
+    version('2.1.0',                sha256='f89c02377d3190950b75fa29b36d91fd2515256434dbe96364eb48bfc3caf832')
+    version('2-0-4',                sha256='27695b68fa33e9b2c3a683ed8fc24bb48b1d6d020bac9aa6c48df20a8aa34d17')
+    version('2-0-3',                sha256='d6e90e9dfdfdabd761f90281a8c8ebeddf2e04443253d093becb60addd0e8897')
+    version('2-0-2',                sha256='ce713ee1ee2c234f9ec00e5d8ba452e0aa682900b74dcd8dfc5ae01fd6342b08')
+    version('2-0-1',                sha256='dcdadb8af35d4348770aef531ab1109c6af77b5f390a8003b5b025e300b7fa7f')
+    version('2.0.0',                sha256='3aaa6274646886d640c362ec8937e5ae3d63c3cdf2a0236ac1dc532e87869f10')
+
+    # FIXME: Add dependencies if required. Only add the python dependency
+    # if you need specific versions. A generic python dependency is
+    # added implicity by the PythonPackage class.
+    depends_on('[email protected]:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-dials-data')
+    depends_on('py-jinja2')
+    depends_on('py-procrunner')
+    depends_on('py-six')
+
+    # tests
+    depends_on('py-pytest-runner', type='test') # add type=test? only needed during development
+    depends_on('py-mock', type='test')
+    depends_on('py-coverage@:4.9', type='test')
+    depends_on('py-pytest', type='test')
+    depends_on('py-pytest-cov', type='test')
+    depends_on('py-testpath', type='test')
+
+
+    def build_args(self, spec, prefix):
+        # FIXME: Add arguments other than --prefix
+        # FIXME: If not needed delete this function
+        args = []
+        return args

packages/py-extra-foam/package.py

@@ -0,0 +1,86 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+# ----------------------------------------------------------------------------
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
+#
+# This is a template package file for Spack.  We've put "FIXME"
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
+#
+#     spack install py-extra-foam
+#
+# You can edit this file again by typing:
+#
+#     spack edit py-extra-foam
+#
+# See the Spack documentation for more information on packaging.
+# ----------------------------------------------------------------------------
+
+from spack import *
+
+
+class PyExtraFoam(PythonPackage):
+    """EXtra-foam is a framework that provides real-time and off-line data analysis 
+    (detector geometry, pump-probe, azimuthal integration, ROI, statistics, etc.) 
+    and visualization for experiments that use 2D area detectors (AGIPD, LPD, DSSC, 
+    FastCCD, JungFrau, ePix100, etc.) and 1D detectors (Gotthard, XGM, digitizer, etc.) 
+    at European XFEL."""
+
+    # FIXME: Add a proper url for your package's homepage here.
+    homepage = "https://extra-foam.readthedocs.io/en/latest/"
+    url      = "https://github.com/European-XFEL/EXtra-foam/archive/1.0.0.tar.gz"
+
+    # FIXME: Add a list of GitHub accounts to
+    # notify when the package is updated.
+    maintainers = ['RobertRosca', 'julianhoersch']
+
+    version('1.0.0beta3', sha256='38e1f7ea05ed32a3d041dbccb85862055436db4374a6c4007847d636ff2c003f')
+    version('1.0.0beta2', sha256='04a5bafcb2af2daf122b94c78219ad857b5ad732f121d443d340f2ab49a26581')
+    version('1.0.0beta1', sha256='938f0006ccb9042d44cc0bd6582ab5d191daf96b7db9c9d7afe8258a6798faf4')
+    version('1.0.0',      sha256='8bb214cb21a414175f9ca207485c6cf6fac9c569198ac59b23b3a023f0f420d8')
+    version('0.9.1',      sha256='7f3c48985d0f656e35e6364a6279e458841566b866c59bd509aa96b855d2d668')
+    version('0.9.0beta3', sha256='fbd3e2b23d9cfc623b225c4572be54b31ef3203597b43ba5a9cb8b1e333f983c')
+    version('0.9.0beta2', sha256='84eddd55220e4e89080442f267141a2688cf5cda397b5e22da6303622c675b4e')
+    version('0.9.0beta1', sha256='b1bbaa7d0edc4064106c10a837bfcf7f345889f51419d558734a292cefe737c7')
+    version('0.9.0',      sha256='aa3422639b6ef6f7cbe0b93155322d51af89115f30a4525104268adbb0fed6f7')
+    version('0.8.4',      sha256='ab36bb07952eb0b4e1956bdb626df0ce3975ab64dc64eda6822ddc5759fb8a14')
+
+    # FIXME: Add dependencies if required. Only add the python dependency
+    # if you need specific versions. A generic python dependency is
+    # added implicity by the PythonPackage class.
+    depends_on('[email protected]:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('[email protected]:')
+    depends_on('[email protected]:')
+    depends_on('[email protected]:')
+    depends_on('[email protected]:')
+    depends_on('[email protected]:')
+    depends_on('[email protected]:')
+    depends_on('[email protected]') # needs higher compiler version as default on maxwell ([email protected]) -> gcc@:5.0.999
+    depends_on('[email protected]:')
+    depends_on('[email protected]:')
+    depends_on('[email protected]:')
+    depends_on('[email protected]:')
+    depends_on('[email protected]:')
+    depends_on('[email protected]')
+    depends_on('[email protected]')
+    depends_on('[email protected]:')
+    depends_on('[email protected]')
+    depends_on('[email protected]')
+    depends_on('[email protected]:')
+
+    depends_on('py-coverage@:4.9', type='test')
+    depends_on('py-pytest', type='test')
+    depends_on('py-pytest-cov', type='test')
+    depends_on('py-testpath', type='test')
+
+
+    def build_args(self, spec, prefix):
+        # FIXME: Add arguments other than --prefix
+        # FIXME: If not needed delete this function
+        args = []
+        return args

packages/py-fabio/package.py

@@ -37,7 +37,7 @@ class PyFabio(PythonPackage):
 
     # FIXME: Add a list of GitHub accounts to
     # notify when the package is updated.
-    maintainers = ['robertrosca']
+    maintainers = ['RobertRosca']
 
     version('0.10.2', sha256='597d7afe414da9b16afeb91439b669d268c8bcfefed1fe400b9a26d93ae58243')
     version('0.10.1', sha256='0c89c5afdead668beae8e79948a6eae7c1d4767c33acde96d68bfe3a2d7dcd96')
@@ -48,6 +48,13 @@ class PyFabio(PythonPackage):
     depends_on('[email protected]:',   type=('build', 'run'))
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy')
+
+    #test dependencies
+    depends_on('py-coverage@:4.9', type='test')
+    depends_on('py-pytest', type='test')
+    depends_on('py-pytest-cov', type='test')
+    depends_on('py-testpath', type='test')
+
     def build_args(self, spec, prefix):
         # FIXME: Add arguments other than --prefix
         # FIXME: If not needed delete this function