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Merged
hattne merged 5 commits into from
Jul 12, 2025
Merged

Install all dependencies with APT, reduce verbosity in Makefile build #91

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00ae064
Install all dependencies with APT
hattne Jun 19, 2025
917bbbc
Reduce verbose output from non-critical commands
hattne Jun 20, 2025
d97c2cb
Use all Docker CPU:s by default for CMake
hattne Jun 20, 2025
12b317c
Use UTF-8 locale inside container
hattne Jun 25, 2025
64fefac
Merge branch 'dials:main' into docker-make
hattne Jul 5, 2025
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5 changes: 3 additions & 2 deletions .dev/docker/cmake_ctest.dockerfile
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
FROM ubuntu:24.04
SHELL ["/bin/bash", "-c"]
ENV LANG=C.UTF-8

RUN mkdir /app
COPY ./cbflib /app/cbflib
Expand All @@ -9,7 +10,7 @@ RUN apt-get update && \

RUN cd /app/cbflib && \
cmake . && \
cmake --build . --parallel 4
cmake --build . --parallel `nproc`

RUN cd /app/cbflib && \
ctest --parallel 4
ctest --parallel `nproc`
16 changes: 2 additions & 14 deletions .dev/docker/make_tests.dockerfile
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@@ -1,29 +1,17 @@
FROM ubuntu:24.04
SHELL ["/bin/bash", "-c"]
ENV LANG=C.UTF-8

RUN mkdir /app
COPY ./cbflib /app/cbflib

RUN apt-get update && \
apt-get install -y bison build-essential git wget libjpeg-dev m4 automake libpcre2-dev liblzma-dev rsync gfortran libz-dev

RUN mkdir -p ~/miniconda3 && \
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh && \
bash ~/miniconda3/miniconda.sh -b -u -p /usr/share/miniconda && \
rm ~/miniconda3/miniconda.sh

RUN source /usr/share/miniconda/etc/profile.d/conda.sh && \
conda create -y -n build -c conda-forge python=3.11 python-build && \
conda create -y -n test -c conda-forge python=3.11 numpy matplotlib
apt-get install -y bison build-essential git wget libjpeg-dev m4 automake libpcre2-dev liblzma-dev python3-build python3-dev python3-numpy-dev python3-setuptools python3-venv rsync gfortran libz-dev

RUN cd /app/cbflib && \
source /usr/share/miniconda/etc/profile.d/conda.sh && \
conda activate build && \
make all

RUN cd /app/cbflib && \
source /usr/share/miniconda/etc/profile.d/conda.sh && \
conda activate test && \
make tests 2>&1 | tee test.out

RUN ! grep -a ignored /app/cbflib/test.out
8 changes: 4 additions & 4 deletions .github/workflows/cmake_ctest.yml
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@@ -1,4 +1,4 @@
name: Cmake build and tests
name: CMake build and tests

on:
push:
Expand All @@ -18,14 +18,14 @@ jobs:

steps:
- uses: actions/checkout@v4
- name: install extra dependencies
- name: Install extra dependencies
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@dwpaley dwpaley Jul 7, 2025

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thank you, maybe my shift key is defective

run: |
sudo apt-get update
sudo apt-get install -y python3-numpy-dev
- name: build
- name: Build
run: |
cmake .
cmake --build . --parallel `nproc`
- name: test
- name: Test
run: |
ctest --parallel `nproc`
20 changes: 5 additions & 15 deletions .github/workflows/make_tests.yml
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Expand Up @@ -12,32 +12,22 @@ on:
schedule:
- cron: '0 20 * * 1' # Monday 20:00 UTC


jobs:
build_test:

runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v4
- name: create conda environments
run: |
conda create -y -n build -c conda-forge python=3.11 python-build
conda create -y -n test -c conda-forge python=3.11 numpy matplotlib
- name: install extra dependencies
- name: Install extra dependencies
run: |
sudo apt-get update
sudo apt-get install -y libjpeg-dev liblzma-dev
- name: build
sudo apt-get install -y libjpeg-dev liblzma-dev python3-build python3-dev python3-numpy-dev
- name: Build
run: |
source /usr/share/miniconda/etc/profile.d/conda.sh
conda activate build
make all
- name: test
- name: Test
run: |
source /usr/share/miniconda/etc/profile.d/conda.sh
conda activate test
make tests 2>&1 | tee test.out
- name : check test output
- name : Check test output
run: |
! grep -a ignored test.out
96 changes: 21 additions & 75 deletions Makefile
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Expand Up @@ -538,11 +538,6 @@ REGEX_INCLUDES ?=
endif


# Program to use to retrieve a URL

DOWNLOAD ?= wget -N
#DOWNLOAD ?= curl -O -L

# Flag to control symlinks versus copying

SLFLAGS = --use_ln
Expand Down Expand Up @@ -1482,7 +1477,6 @@ $(SWIG_FORTRAN_KIT): build_swig_fortran
git clone $(SWIG_FORTRAN_URL) $(SWIG_FORTRAN_KIT)
(export SWIG_FORTRAN_PREFIX=$(PWD);cd $(SWIG_FORTRAN_KIT); ./autogen.sh; \
./configure --prefix=$(F90CBF); make; make install)
touch $(SWIG_FORTRAN_KIT)
endif

ifneq ($(CBFLIB_DONT_USE_LOCAL_SWIG),yes)
Expand All @@ -1496,7 +1490,6 @@ $(SWIG_KIT): build_swig
git clone $(SWIG_URL) $(SWIG_KIT)
(export SWIG_PREFIX=$(PWD);cd $(SWIG_KIT); ./autogen.sh; \
./configure --prefix=$(SWIG_PREFIX); make; make install)
touch $(SWIG_KIT)
endif


Expand All @@ -1508,10 +1501,7 @@ build_py2cifrw: $(M4)/Makefile.m4
touch build_py2cifrw
$(PY2CIFRW): build_py2cifrw
-rm -rf $(PY2CIFRW)
-rm -rf $(PY2CIFRW).tar.gz
$(DOWNLOAD) $(PY2CIFRWURL)
tar -xvf $(PY2CIFRW).tar.gz
-rm $(PY2CIFRW).tar.gz
wget -O - -nv $(PY2CIFRWURL) | tar -xzf -
(cd $(PY2CIFRW); \
PYTHONPATH=$(PY2CIFRW_PREFIX)/lib/python:$(PY2CIFRW_PREFIX)/lib64/python; export PYTHONPATH; \
mkdir -p $(PY2CIFRW_PREFIX)/lib/python/site-packages; \
Expand All @@ -1525,10 +1515,7 @@ build_py2ply: $(M4)/Makefile.m4
touch build_py2ply
$(PY2PLY): build_py2ply
-rm -rf $(PY2PLY)
-rm -rf $(PY2PLY).tar.gz
$(DOWNLOAD) $(PY2PLYURL)
tar -xvf $(PY2PLY).tar.gz
-rm $(PY2PLY).tar.gz
wget -O - -nv $(PY2PLYURL) | tar -xzf -
(cd $(PY2PLY); \
PYTHONPATH=$(PY2CIFRW_PREFIX)/lib/python:$(PY2CIFRW_PREFIX)/lib64/python; export PYTHONPATH; \
mkdir -p $(PY2CIFRW_PREFIX)/lib/python/site-packages; \
Expand All @@ -1544,10 +1531,7 @@ build_py3cifrw: $(M4)/Makefile.m4
touch build_py3cifrw
$(PY3CIFRW): build_py3cifrw
-rm -rf $(PY3CIFRW)
-rm -rf $(PY3CIFRW).tar.gz
$(DOWNLOAD) $(PY3CIFRWURL)
tar -xvf $(PY3CIFRW).tar.gz
-rm $(PY3CIFRW).tar.gz
wget -O - -nv $(PY3CIFRWURL) | tar -xf -
(cd $(PY3CIFRW); \
PYTHONPATH=$(PY3CIFRW_PREFIX)/lib/python:$(PY3CIFRW_PREFIX)/lib64/python; export PYTHONPATH; \
mkdir -p $(PY3CIFRW_PREFIX)/lib/python/site-packages; \
Expand All @@ -1561,10 +1545,7 @@ build_py3ply: $(M4)/Makefile.m4
touch build_py3ply
$(PY3PLY): build_py3ply
-rm -rf $(PY3PLY)
-rm -rf $(PY3PLY).tar.gz
$(DOWNLOAD) $(PY3PLYURL)
tar -xvf $(PY3PLY).tar.gz
-rm $(PY3PLY).tar.gz
wget -O - -nv $(PY3PLYURL) | tar -xzf -
(cd $(PY3PLY); \
PYTHONPATH=$(PY3CIFRW_PREFIX)/lib/python:$(PY3CIFRW_PREFIX)/lib64/python; export PYTHONPATH; \
mkdir -p $(PY3CIFRW_PREFIX)/lib/python/site-packages; \
Expand All @@ -1579,11 +1560,7 @@ endif
ifneq ($(NUWEB_DEP),'')
$(NUWEB_DEP):
-rm -rf $(NUWEB_DEP)
-rm -rf $(NUWEB_DEP).tar.gz
$(DOWNLOAD) $(NUWEB_URL)
tar -xvf $(NUWEB_DEP).tar.gz
touch $(NUWEB_DEP)
rm $(NUWEB_DEP).tar.gz
wget -O - -nv $(NUWEB_URL) | tar -xzf -

$(NUWEB_DEP2): $(NUWEB_DEP)
(cd $(NUWEB_DEP); make nuweb; cp nuweb $(NUWEB_DEP2))
Expand All @@ -1598,19 +1575,15 @@ build_regex: $(M4)/Makefile.m4
touch build_regex
$(REGEX): build_regex
-rm -rf $(REGEX)
-rm -rf $(REGEX).tar.gz
$(DOWNLOAD) $(REGEX_URL)
tar -xvf $(REGEX).tar.gz
touch $(REGEX)
-rm $(REGEX).tar.gz
wget -O - -nv $(REGEX_URL) | tar -xzf -
cp config.guess config.sub $(REGEX)
(cd $(REGEX); \
prefix=$(REGEX_PREFIX); export prefix; \
./configure --prefix=$(REGEX_PREFIX); make install)
@-cp $(REGEX_PREFIX)/include/pcre2posix.h $(REGEX_PREFIX)/include/regex.h
$(REGEX)_INSTALL: $(REGEX)
-rm -rf $(REGEX)_install
rsync -avz $(REGEX)/ $(REGEX)_install
rsync -az $(REGEX)/ $(REGEX)_install
(cd $(REGEX)_install; prefix=$(CBF_PREFIX); export prefix; \
make distclean; ./configure --prefix=$(CBF_PREFIX); make install )
@-cp $(CBF_PREFIX)/include/pcre2posix.h $(CBF_PREFIX)/include/regex.h
Expand All @@ -1622,17 +1595,13 @@ build_tiff: $(M4)/Makefile.m4
touch build_tiff
$(TIFF): build_tiff config.guess config.sub
-rm -rf $(TIFF)
-rm -rf $(TIFF).tar.gz
$(DOWNLOAD) $(TIFF_URL)
tar -xvf $(TIFF).tar.gz
touch $(TIFF)
-rm $(TIFF).tar.gz
wget -O - -nv $(TIFF_URL) | tar -xzf -
cp config.guess config.sub $(TIFF)/config/
(cd $(TIFF); prefix=$(TIFF_PREFIX); export prefix; \
./configure --prefix=$(TIFF_PREFIX); make install)
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
rsync -az $(TIFF)/ $(TIFF)_install
(cd $(TIFF)_install; make distclean; prefix=$(CBF_PREFIX); export prefix; \
./configure --prefix=$(CBF_PREFIX); make install)

Expand All @@ -1646,30 +1615,26 @@ build_hdf5: $(M4)/Makefile.m4
touch build_hdf5
$(HDF5): build_hdf5 $(LIBAECdep)
-rm -rf $(HDF5)
-rm -rf $(HDF5).tar.gz
$(DOWNLOAD) $(HDF5_URL)
tar -xvf $(HDF5).tar.gz
wget -O - -nv $(HDF5_URL) | tar -xzf -
cp config.guess $(HDF5)/bin/config.guess
cp config.sub $(HDF5)/bin/config.sub
touch $(HDF5)
-rm $(HDF5).tar.gz
echo "first level HDF5 install in "$(HDF5_PREFIX)
(cd $(ROOT)/$(HDF5); \
CFLAGS="$(CFLAGS)"; export CFLAGS; \
mkdir -p hdf5; prefix=$(ROOT)/$(HDF5)/hdf5; export prefix; \
./configure --prefix=$(ROOT)/$(HDF5)/hdf5 --enable-build-mode=production \
--enable-trace --enable-fortran --enable-using-memchecker --with-szlib=$(ROOT) ;\
make install; \
rsync -avz $(ROOT)/$(HDF5)/hdf5/bin/ $(HDF5_PREFIX)/bin; \
rsync -avz $(ROOT)/$(HDF5)/hdf5/lib/ $(HDF5_PREFIX)/lib; \
rsync -avz $(ROOT)/$(HDF5)/hdf5/include/ $(HDF5_PREFIX)/include; \
rsync -az $(ROOT)/$(HDF5)/hdf5/bin/ $(HDF5_PREFIX)/bin; \
rsync -az $(ROOT)/$(HDF5)/hdf5/lib/ $(HDF5_PREFIX)/lib; \
rsync -az $(ROOT)/$(HDF5)/hdf5/include/ $(HDF5_PREFIX)/include; \
cd $(HDF5_PREFIX)/bin; $(ROOT)/$(HDF5)/hdf5/bin/h5redeploy -force )
$(HDF5)_INSTALL: $(HDF5)
-rm -rf $(HDF5)_install
echo "final HDF5 install in "$(CBF_PREFIX)
rsync -avz $(ROOT)/$(HDF5)/hdf5/bin/ $(CBF_PREFIX)/bin; \
rsync -avz $(ROOT)/$(HDF5)/hdf5/lib/ $(CBF_PREFIX)/lib; \
rsync -avz $(ROOT)/$(HDF5)/hdf5/include/ $(CBF_PREFIX)/include; \
rsync -az $(ROOT)/$(HDF5)/hdf5/bin/ $(CBF_PREFIX)/bin; \
rsync -az $(ROOT)/$(HDF5)/hdf5/lib/ $(CBF_PREFIX)/lib; \
rsync -az $(ROOT)/$(HDF5)/hdf5/include/ $(CBF_PREFIX)/include; \
cd $(CBF_PREFIX)/bin; $(ROOT)/$(HDF5)/hdf5/bin/h5redeploy -force
endif

Expand All @@ -1682,13 +1647,9 @@ build_libaec: $(M4)/Makefile.m4
$(LIBAEC): build_libaec
mkdir -p $(SOLIB)
-rm -rf $(LIBAEC)
-rm -rf $(LIBAEC).tar.gz
$(DOWNLOAD) $(LIBAEC_URL)
tar -xvf $(LIBAEC).tar.gz
-rm $(LIBAEC).tar.gz
wget -O - -nv $(LIBAEC_URL) | tar -xzf -
(cd $(LIBAEC); mkdir -p build; cd build; ../configure --prefix=$(ROOT); make install; \
cp $(LIB)/libsz.so* $(LIB)/libaec.so* $(SOLIB))
touch $(LIBAEC)
endif

ifneq ($(CBFLIB_DONT_USE_LZ4),yes)
Expand All @@ -1701,10 +1662,7 @@ $(LZ4): $(HDF5) build_lz4
mkdir -p $(SOLIB)
-rm -rf $(LZ4)
ifneq ($(MSYS2),yes)
-rm -rf $(LZ4).tar.gz
$(DOWNLOAD) $(LZ4_URL)
tar -xvf $(LZ4).tar.gz
-rm $(LZ4).tar.gz
wget -O - -nv $(LZ4_URL) | tar -xzf -
(cp $(LZ4include)/lz4.h $(INCLUDE); \
$(CC) $(CFLAGS) $(SOWCFLAGS) $(INCLUDES) $(WARNINGS) -c $(LZ4src)/lz4.c -o lz4.o; \
$(CC) $(CFLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(LZ4src)/h5zlz4.c -o h5zlz4.o; \
Expand All @@ -1714,7 +1672,6 @@ else
git clone $(LZ4_URL)
(cd $(LZ4); mkdir build; cd build; cmake .. -G 'MSYS Makefiles' -DENABLE_LZ4_PLUGIN="yes"; make all; cp plugins/* $(SOLIB))
endif
touch $(LZ4)
endif


Expand All @@ -1730,7 +1687,6 @@ $(BSHUF): $(HDF5) build_BSHUF $(LZ4dep)
git clone $(BSHUF_URL)
(cd $(BSHUF); git submodule update --init; $(PYTHON3) -m build --config-setting=install \
-C--h5plugin -C--h5plugin-dir=../solib -C--zstd -C--user)
touch $(BSHUF)
endif

ifneq ($(CBFLIB_DONT_USE_ZSTD),yes)
Expand All @@ -1750,7 +1706,6 @@ $(ZSTD): $(HDF5) build_ZSTD
$(CC) -shared zstd_h5plugin.o $(HDF5SOLIBS_LOCAL) $(HDF5SOLIBS_SYSTEM) -lzstd \
-o $(SOLIB)/$(ZSTDFILTER).so; \
rm zstd_h5plugin.o)
touch $(ZSTD)
endif

ifneq ($(CBFLIB_DONT_USE_CQRLIB),yes)
Expand All @@ -1772,7 +1727,6 @@ cqrlib $(SOLIB)/libcqr.so $(LIB)lbcqr.a: build_CQRLIB
ifneq ($(RANLIB),)
$(RANLIB) $(LIB)/libcqr.a
endif
touch cqrlib
endif


Expand Down Expand Up @@ -1952,7 +1906,6 @@ $(PY2CBF)/xmas/readmarheader.py \
$(PY2CBF)/xmas/xmasheaders.py \
$(PY2CBF)/xmas/xmas_cif_template.cif : $(NUWEB_DEP) $(NUWEB_DEP2) $(PY2CBF)/pycbf.w
(cd $(PY2CBF); $(NUWEB) pycbf.w )
touch $(PY2CBF)/py2setup_py.m4

$(PY2CBF)/_py2cbf.$(PY2CBFEXT): $(PY2CBF) shared \
$(PY2CBF)/py2setup.py \
Expand Down Expand Up @@ -2024,7 +1977,6 @@ $(PY3CBF)/xmas/readmarheader.py \
$(PY3CBF)/xmas/xmasheaders.py \
$(PY3CBF)/xmas/xmas_cif_template.cif: $(NUWEB_DEP) $(NUWEB_DEP2) $(PY3CBF)/pycbf.w
(cd $(PY3CBF); $(NUWEB) pycbf.w )
touch $(PY3CBF)/py3setup_py.m4


$(PY3CBF)/_pycbf.$(PY3CBFEXT): $(PY3CBF) shared \
Expand Down Expand Up @@ -2484,16 +2436,10 @@ $(BIN)/cbf_testxfelread: $(LIB)/libcbf.a $(EXAMPLES)/cbf_testxfelread.c $(EXAMPL
#

$(DATADIRI): $(M4)/Makefile.m4
(cd ..; $(DOWNLOAD) $(DATAURLI))
(cd ..; tar -zxvf CBFlib_$(VERSION)_Data_Files_Input.tar.gz)
touch $(DATADIRI)
-(cd ..; rm CBFlib_$(VERSION)_Data_Files_Input.tar.gz)
wget -O - -nv $(DATAURLI) | tar -C .. -xzf -

$(DATADIRO): $(M4)/Makefile.m4
(cd ..; $(DOWNLOAD) $(DATAURLO))
(cd ..; tar -zxvf CBFlib_$(VERSION)_Data_Files_Output.tar.gz)
touch $(DATADIRO)
-(cd ..; rm CBFlib_$(VERSION)_Data_Files_Output.tar.gz)
wget -O - -nv $(DATAURLO) | tar -C .. -xzf -

# Input Data Files

Expand Down Expand Up @@ -3174,7 +3120,7 @@ tar: $(DOCUMENTS) $(SOURCE) $(SRC)/cbf.stx $(HEADERS) $(M4FILES)\
README.html README Makefile \
$(JPEGS)
-/bin/rm -f CBFlib.tar*
tar cvBf CBFlib.tar \
tar -cf CBFlib.tar \
$(DOCUMENTS) $(SOURCE) $(SRC)/cbf.stx $(HEADERS) $(M4FILES)\
$(EXAMPLES) \
README.html README Makefile \
Expand Down
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