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Add notes on installing as user vs developer, and with conda
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| ============ | ||
| Installation | ||
| ============ | ||
|
|
||
| First, you'll need to have the required C libraries: ``gsl``, ``fftw`` (make sure | ||
| you install the floating-point version!) | ||
| ``openmp`` and ``gslcblas``. | ||
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||
| Then follow the instructions below, depending on whether you are a user or a developer. | ||
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| For Users | ||
| --------- | ||
|
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| .. note:: `conda` users may want to pre-install the following packages before running | ||
| the below installation commands:: | ||
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| conda install numpy scipy click pyyaml cffi astropy h5py | ||
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| Then, at the command line:: | ||
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| pip install git+git://github.com/21cmFAST/21cmFAST.git | ||
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| If developing, from the top-level directory do:: | ||
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| pip install -e . | ||
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| Note the compile options discussed below! | ||
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| For Developers | ||
| -------------- | ||
| If you are developing `21cmFAST`, we highly recommend using `conda` to manage your | ||
| environment, and setting up an isolated environment. If this is the case, setting up | ||
| a full environment (with all testing and documentation dependencies) should be as easy | ||
| as (from top-level dir):: | ||
|
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| conda env create -f environment_dev.yml | ||
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| Otherwise, if you are using `pip`:: | ||
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| pip install -e . | ||
| pip install -r requirements_dev.txt | ||
|
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| And if you would like to also compile documentation:: | ||
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| pip install -r docs/requirements.txt | ||
|
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||
| Compile Options | ||
| --------------- | ||
| Various options exist to manage compilation via environment variables. Basically, | ||
| any variable with "INC" in its name will add to the includes directories, while | ||
| any variable with "lib" in its name will add to the directories searched for | ||
| libraries. To change the C compiler, use ``CC``. Finally, if you want to compile | ||
| the C-library in dev mode (so you can do stuff like valgrid and gdb with it), | ||
| install with DEBUG=True. So for example:: | ||
|
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| CC=/usr/bin/gcc DEBUG=True GSL_LIB=/opt/local/lib FFTW_INC=/usr/local/include pip install -e . | ||
|
|
||
| In addition, the ``BOXDIR`` variable specifies the *default* directory that any | ||
| data produced by 21cmFAST will be cached. This value can be updated at any time by | ||
| changing it in the ``$CFGDIR/config.yml`` file, and can be overwritten on a | ||
| per-call basis. | ||
|
|
||
| While the ``-e`` option will keep your library up-to-date with any (Python) | ||
| changes, this will *not* work when changing the C extension. If the C code | ||
| changes, you need to manually run ``rm -rf build/*`` then re-install as above. | ||
|
|
||
| Logging in C-Code | ||
| ~~~~~~~~~~~~~~~~~ | ||
| By default, the C-code will only print to stderr when it encounters warnings or | ||
| critical errors. However, there exist several levels of logging output that can be | ||
| switched on, but only at compilation time. To enable these, use the following:: | ||
|
|
||
| LOG_LEVEL=<log_level> pip install -e . | ||
|
|
||
| The ``<log_level>`` can be any non-negative integer, or one of the following | ||
| (case-insensitive) identifiers:: | ||
|
|
||
| NONE, ERROR, WARNING, INFO, DEBUG, SUPER_DEBUG, ULTRA_DEBUG | ||
|
|
||
| If an integer is passed, it corresponds to the above levels in order (starting | ||
| from zero). Be careful if the level is set to 0 (or NONE), as useful error | ||
| and warning messages will not be printed. By default, the log level is 2 (or | ||
| WARNING), unless the DEBUG=1 environment variable is set, in which case the | ||
| default is 4 (or DEBUG). Using very high levels (eg. ULTRA_DEBUG) can print out | ||
| *a lot* of information and make the run time much longer, but may be useful | ||
| in some specific cases. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,54 +1 @@ | ||
| ============ | ||
| Installation | ||
| ============ | ||
|
|
||
| First, you'll need to have the required C libraries: ``gsl``, ``fftw`` (make sure | ||
| you install the floating-point version!) | ||
| ``openmp`` and ``gslcblas``. | ||
|
|
||
| Then, at the command line:: | ||
|
|
||
| pip install 21cmFAST | ||
|
|
||
| If developing, from the top-level directory do:: | ||
|
|
||
| pip install -e . | ||
|
|
||
| Various options exist to manage compilation via environment variables. Basically, | ||
| any variable with "INC" in its name will add to the includes directories, while | ||
| any variable with "lib" in its name will add to the directories searched for | ||
| libraries. To change the C compiler, use ``CC``. Finally, if you want to compile | ||
| the C-library in dev mode (so you can do stuff like valgrid and gdb with it), | ||
| install with DEBUG=True. So for example:: | ||
|
|
||
| CC=/usr/bin/gcc DEBUG=True GSL_LIB=/opt/local/lib FFTW_INC=/usr/local/include pip install -e . | ||
|
|
||
| In addition, the ``BOXDIR`` variable specifies the *default* directory that any | ||
| data produced by 21cmFAST will be cached. This value can be updated at any time by | ||
| changing it in the ``$CFGDIR/config.yml`` file, and can be overwritten on a | ||
| per-call basis. | ||
|
|
||
| While the ``-e`` option will keep your library up-to-date with any (Python) | ||
| changes, this will *not* work when changing the C extension. If the C code | ||
| changes, you need to manually run ``rm -rf build/*`` then re-install as above. | ||
|
|
||
| Logging in C-Code | ||
| ----------------- | ||
| By default, the C-code will only print to stderr when it encounters warnings or | ||
| critical errors. However, there exist several levels of logging output that can be | ||
| switched on, but only at compilation time. To enable these, use the following:: | ||
|
|
||
| LOG_LEVEL=<log_level> pip install -e . | ||
|
|
||
| The ``<log_level>`` can be any non-negative integer, or one of the following | ||
| (case-insensitive) identifiers:: | ||
|
|
||
| NONE, ERROR, WARNING, INFO, DEBUG, SUPER_DEBUG, ULTRA_DEBUG | ||
|
|
||
| If an integer is passed, it corresponds to the above levels in order (starting | ||
| from zero). Be careful if the level is set to 0 (or NONE), as useful error | ||
| and warning messages will not be printed. By default, the log level is 2 (or | ||
| WARNING), unless the DEBUG=1 environment variable is set, in which case the | ||
| default is 4 (or DEBUG). Using very high levels (eg. ULTRA_DEBUG) can print out | ||
| *a lot* of information and make the run time much longer, but may be useful | ||
| in some specific cases. | ||
| .. include:: ../INSTALLATION.rst |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| name: 21cmfast | ||
| channels: | ||
| - defaults | ||
| dependencies: | ||
| - alabaster=0.7.12=py37_0 | ||
| - asn1crypto=0.24.0=py37_0 | ||
| - astropy=3.2=py37h7b6447c_0 | ||
| - atomicwrites=1.3.0=py37_1 | ||
| - attrs=19.1.0=py37_1 | ||
| - babel=2.7.0=py_0 | ||
| - backcall=0.1.0=py37_0 | ||
| - blas=1.0=mkl | ||
| - ca-certificates=2019.5.15=0 | ||
| - certifi=2019.3.9=py37_0 | ||
| - cffi=1.12.3=py37h2e261b9_0 | ||
| - chardet=3.0.4=py37_1 | ||
| - click=7.0=py37_0 | ||
| - cryptography=2.7=py37h1ba5d50_0 | ||
| - cycler=0.10.0=py37_0 | ||
| - dbus=1.13.6=h746ee38_0 | ||
| - decorator=4.4.0=py37_1 | ||
| - docutils=0.14=py37_0 | ||
| - expat=2.2.6=he6710b0_0 | ||
| - fontconfig=2.13.0=h9420a91_0 | ||
| - freetype=2.9.1=h8a8886c_1 | ||
| - glib=2.56.2=hd408876_0 | ||
| - gst-plugins-base=1.14.0=hbbd80ab_1 | ||
| - gstreamer=1.14.0=hb453b48_1 | ||
| - icu=58.2=h9c2bf20_1 | ||
| - idna=2.8=py37_0 | ||
| - imagesize=1.1.0=py37_0 | ||
| - importlib_metadata=0.17=py37_1 | ||
| - intel-openmp=2019.4=243 | ||
| - ipython=7.5.0=py37h39e3cac_0 | ||
| - ipython_genutils=0.2.0=py37_0 | ||
| - jedi=0.13.3=py37_0 | ||
| - jinja2=2.10.1=py37_0 | ||
| - jpeg=9b=h024ee3a_2 | ||
| - kiwisolver=1.1.0=py37he6710b0_0 | ||
| - libedit=3.1.20181209=hc058e9b_0 | ||
| - libffi=3.2.1=hd88cf55_4 | ||
| - libgcc-ng=9.1.0=hdf63c60_0 | ||
| - libgfortran-ng=7.3.0=hdf63c60_0 | ||
| - libpng=1.6.37=hbc83047_0 | ||
| - libstdcxx-ng=9.1.0=hdf63c60_0 | ||
| - libuuid=1.0.3=h1bed415_2 | ||
| - libxcb=1.13=h1bed415_1 | ||
| - libxml2=2.9.9=he19cac6_0 | ||
| - markupsafe=1.1.1=py37h7b6447c_0 | ||
| - matplotlib=3.1.0=py37h5429711_0 | ||
| - mkl=2019.4=243 | ||
| - mkl_fft=1.0.12=py37ha843d7b_0 | ||
| - mkl_random=1.0.2=py37hd81dba3_0 | ||
| - more-itertools=7.0.0=py37_0 | ||
| - ncurses=6.1=he6710b0_1 | ||
| - numpy=1.16.4=py37h7e9f1db_0 | ||
| - numpy-base=1.16.4=py37hde5b4d6_0 | ||
| - numpydoc=0.9.1=py_0 | ||
| - openssl=1.1.1c=h7b6447c_1 | ||
| - packaging=19.0=py37_0 | ||
| - parso=0.4.0=py_0 | ||
| - pcre=8.43=he6710b0_0 | ||
| - pexpect=4.7.0=py37_0 | ||
| - pickleshare=0.7.5=py37_0 | ||
| - pip=19.1.1=py37_0 | ||
| - pluggy=0.12.0=py_0 | ||
| - prompt_toolkit=2.0.9=py37_0 | ||
| - psutil=5.6.2=py37h7b6447c_0 | ||
| - ptyprocess=0.6.0=py37_0 | ||
| - py=1.8.0=py37_0 | ||
| - pycparser=2.19=py37_0 | ||
| - pygments=2.4.2=py_0 | ||
| - pyopenssl=19.0.0=py37_0 | ||
| - pyparsing=2.4.0=py_0 | ||
| - pyqt=5.9.2=py37h05f1152_2 | ||
| - pysocks=1.7.0=py37_0 | ||
| - pytest=4.6.2=py37_0 | ||
| - pytest-arraydiff=0.3=py37h39e3cac_0 | ||
| - pytest-astropy=0.5.0=py37_0 | ||
| - pytest-doctestplus=0.3.0=py37_0 | ||
| - pytest-openfiles=0.3.2=py37_0 | ||
| - pytest-remotedata=0.3.1=py37_0 | ||
| - python=3.7.3=h0371630_0 | ||
| - python-dateutil=2.8.0=py37_0 | ||
| - pytz=2019.1=py_0 | ||
| - pyyaml=5.1=py37h7b6447c_0 | ||
| - qt=5.9.7=h5867ecd_1 | ||
| - readline=7.0=h7b6447c_5 | ||
| - requests=2.22.0=py37_0 | ||
| - scipy=1.2.1=py37h7c811a0_0 | ||
| - setuptools=41.0.1=py37_0 | ||
| - sip=4.19.8=py37hf484d3e_0 | ||
| - six=1.12.0=py37_0 | ||
| - snowballstemmer=1.2.1=py37_0 | ||
| - sphinx=2.1.0=py_0 | ||
| - sphinxcontrib-applehelp=1.0.1=py_0 | ||
| - sphinxcontrib-devhelp=1.0.1=py_0 | ||
| - sphinxcontrib-htmlhelp=1.0.2=py_0 | ||
| - sphinxcontrib-jsmath=1.0.1=py_0 | ||
| - sphinxcontrib-qthelp=1.0.2=py_0 | ||
| - sphinxcontrib-serializinghtml=1.1.3=py_0 | ||
| - sqlite=3.28.0=h7b6447c_0 | ||
| - tk=8.6.8=hbc83047_0 | ||
| - toml=0.10.0=py37h28b3542_0 | ||
| - tornado=6.0.2=py37h7b6447c_0 | ||
| - tqdm=4.32.1=py_0 | ||
| - traitlets=4.3.2=py37_0 | ||
| - urllib3=1.24.2=py37_0 | ||
| - wcwidth=0.1.7=py37_0 | ||
| - wheel=0.33.4=py37_0 | ||
| - xz=5.2.4=h14c3975_4 | ||
| - yaml=0.1.7=had09818_2 | ||
| - zipp=0.5.1=py_0 | ||
| - zlib=1.2.11=h7b6447c_3 | ||
| - pip: | ||
| - aspy-yaml==1.3.0 | ||
| - bleach==3.1.0 | ||
| - cfgv==2.0.0 | ||
| - coverage==4.5.3 | ||
| - defusedxml==0.6.0 | ||
| - entrypoints==0.3 | ||
| - filelock==3.0.12 | ||
| - identify==1.4.4 | ||
| - jsonschema==3.0.1 | ||
| - jupyter-core==4.4.0 | ||
| - mistune==0.8.4 | ||
| - nbconvert==5.5.0 | ||
| - nbformat==4.4.0 | ||
| - nbsphinx==0.4.2 | ||
| - nodeenv==1.3.3 | ||
| - pandocfilters==1.4.2 | ||
| - pre-commit==1.17.0 | ||
| - pyrsistent==0.15.2 | ||
| - pytest-cov==2.7.1 | ||
| - sphinx-rtd-theme==0.4.3 | ||
| - testpath==0.4.2 | ||
| - tox==3.12.1 | ||
| - virtualenv==16.6.0 | ||
| - webencodings==0.5.1 | ||
|
|
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