Conda #112

paskino · 2018-04-26T05:41:41Z

initial working recipe for linux.

OSX would need tweak on build.sh.

The branch should be aligned with setup_py #109

- depends on SyneRBI/SIRF#161 - fixes (partially) #107 - TODO: alias p(Gadgetron|STIR|Utilities) -> sirf.p* - perhaps use `setup.py install` not `pip install`? - or drop `-e` argument in `pip install`?

- depends on SyneRBI/SIRF#160 - fixes #107

casperdcl · 2018-04-26T08:31:09Z

merge Fix python dest SIRF#160
merge expose python strategy #109
rebase this and merge

close #106?

paskino · 2018-04-26T10:58:40Z

I agree with you.

currently the boost in conda-forge does not contain all the libs we need. So we need to build and install.

KrisThielemans · 2018-04-27T08:43:09Z

should we add a conda build to Travis? Maybe it's already done via the docker build.

that'd allow you to test on OSX.

casperdcl · 2018-04-27T15:19:49Z

EDIT new strategy:

@paskino merge Fix python dest SIRF#160 (no dependencies)
@casperdcl rebase and merge sirf python packaging SIRF#163 (no dependencies)
@paskino @casperdcl rebase and merge this (Conda #112, depends on both the above)

misc:

add conda build to travis (I think getting on conda-forge would avoid this)
close Fix python dest #106

paskino · 2019-07-09T21:03:13Z

Directories to pass to External_SIRF.cmake are defined

For STIR here
NIFTYREG here
ITK (needed by STIR) where?

version 2.1.0

KrisThielemans

I haven't checked this really, but I'm confused about the various build.sh files, and then sirf/build.sh building other stuff anyway.

KrisThielemans · 2019-11-28T11:17:26Z

conda/boost/build.sh

@@ -0,0 +1,72 @@
+#!/bin/bash


I would try to avoid building boost at all costs. Use the conda dependency

KrisThielemans · 2019-11-28T11:18:20Z

conda/hdf5/build.sh

@@ -0,0 +1,79 @@
+#!/bin/bash


let's not build hdf5

KrisThielemans · 2019-11-28T11:19:53Z

conda/ismrmrd/build.sh

+    -DPYTHON_DEST_DIR=${PREFIX}/python\
+    -USIRF_URL \
+    -USIRF_TAG \
+    -DSIRF_TAG=v2.1.0\


let's not put explicit versions in any of the conda build.sh. In any case, SIRF version is irrelevant in ismrmrd/build.sh

KrisThielemans · 2019-11-28T11:21:11Z

conda/sirf/build.sh

+make -j2 ITK
+make -j2 NIFTYREG
+make -j2 STIR


no need for these.

KrisThielemans · 2019-11-28T11:21:52Z

conda/stir/build.sh

+    -DUSE_SYSTEM_GTest=On\
+    -DCONDA_BUILD=On
+
+make  -j1 Gadgetron


in stir/build.sh?

KrisThielemans · 2020-05-11T08:07:19Z

STIR 4.0.1 conda might work ok. There's https://anaconda.org/inati/ismrmrd but it's out-of-date. Might be worth checking with them.

KrisThielemans · 2020-05-11T08:08:55Z

By the way, I'm not 100% sure what the strategy here was/is, but I think we should have a SIRF-only conda package (with its dependencies, most obtained via conda). I would at least initially not attempt gadgetron-via-conda.

KrisThielemans · 2022-01-05T14:39:23Z

See gadgetron/gadgetron#1036 for Gadgetron's conda efforts

KrisThielemans · 2022-09-02T21:21:59Z

conda-recipe/meta.yaml

+    - vc 14 # [win and py35]
+    - vc 9  # [win and py27]
+    - python 3.6 # [py36]
+    - python 2.7 # [py27]


drop this of course

paskino and others added 22 commits April 5, 2018 15:46

first working conda recipe

1c2bd46

use PYTHON_DEST to point to the site_packages

a283c0c

do not overwrite the PYTHON_DEST?

7dbd1c8

removed messages

1585c6d

updated about, removed SIRF_VERSION env var

d2e1615

pulls the 1.0.0 tag

cd54fe9

removed SIRF_VERSION env var

234ab0e

initial setup.py

ed2c6a1

- depends on SyneRBI/SIRF#161 - fixes (partially) #107 - TODO: alias p(Gadgetron|STIR|Utilities) -> sirf.p* - perhaps use `setup.py install` not `pip install`? - or drop `-e` argument in `pip install`?

backward-compatible setup.py

f4ccbf6

- depends on SyneRBI/SIRF#160 - fixes #107

Merge remote-tracking branch 'origin/setup_py' into conda

143c847

missing packages

32b1332

added missing package

9adb67d

bugfixes

a167583

Merge remote-tracking branch 'origin/setup_py' into conda

7057402

bugfixes

e84622f

copies the .so into the site-packages

7495207

copies the .so into the site-packages

011cc36

pip -> setup.py

1f74917

missing docker devel cache

08a9712

pyvenv -> miniconda

9c32624

added dependency

6493243

Merge remote-tracking branch 'origin/setup_py' into conda

3e060be

paskino requested review from KrisThielemans and casperdcl April 26, 2018 05:41

removed boost dependency

04f6d8f

currently the boost in conda-forge does not contain all the libs we need. So we need to build and install.

casperdcl mentioned this pull request Apr 26, 2018

Fix python dest #106

Closed

casperdcl force-pushed the master branch from 30a151b to 025b2aa Compare March 28, 2019 21:12

Merge remote-tracking branch 'origin' into conda

fd94dce

paskino added 13 commits July 12, 2019 10:10

fixed dependency

a97725b

changed SIRF version; add ITK

50a83b6

allows build of Zlib if not present on system

8fc0f85

updated gadgetron version

ee5e5d8

added build variants file

3e7c6c5

added hdf5

d5421d3

additional fixes

63051ae

updated recipe

9901082

added build variants for armadillo

0ece523

Merge tag 'v2.1.0' into conda

c60fffd

version 2.1.0

require Boost 1.68

eadc5f5

install in CONDA build environment

6499445

fix run boost requirement

d4b0c4b

KrisThielemans requested changes Nov 28, 2019

View reviewed changes

paskino added 3 commits November 28, 2019 16:25

updated version strings

c782334

added niftyreg

3770aaa

updated meta

d0d3b74

paskino marked this pull request as draft April 26, 2020 20:11

paskino added 5 commits February 14, 2021 21:20

Merge remote-tracking branch 'origin' into conda

e54fe60

work in progress

113fa93

added missing_dso_whitelist

3e3ec95

add _openmp_mutex

e626863

updated recipes

6ead04e

KrisThielemans reviewed Sep 2, 2022

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Conda #112

Conda #112

paskino commented Apr 26, 2018

casperdcl commented Apr 26, 2018

paskino commented Apr 26, 2018

KrisThielemans commented Apr 27, 2018

casperdcl commented Apr 27, 2018 •

edited by paskino

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Conda #112

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Conda #112

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paskino commented Apr 26, 2018

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casperdcl commented Apr 27, 2018 •

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