diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index caf7554..c476df4 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -28,27 +28,12 @@ jobs: - uses: actions/checkout@v2 - - name: Cache conda pacakges - uses: actions/cache@v2 - env: - # Increase this value to reset cache if etc/example-environment.yml has not changed - CACHE_NUMBER: 0 - with: - path: ~/conda_pkgs_dir - key: - conda-${{ steps.detect.outputs.platform }}-${{ env.CACHE_NUMBER }}-${{hashFiles('conda-lock.yml') }} - - name: Set up conda environment - uses: conda-incubator/setup-miniconda@v2 + uses: mamba-org/setup-micromamba@v1 with: - auto-update-conda: false - activate-environment: test-env - environment-file: conda-${{ steps.detect.outputs.platform }}.lock - - - name: Install pip deps - run: | - cat conda-${{ steps.detect.outputs.platform }}.lock | awk '/^# pip/ {print substr($0,7)}' > requirements.txt - pip install --no-deps -r requirements.txt + environment-file: conda-lock.yml + environment-name: ci + create-args: --category main dev - name: Install project env: diff --git a/README.md b/README.md index 39007ae..7a06358 100644 --- a/README.md +++ b/README.md @@ -18,17 +18,19 @@ sensitivities in different units depending on context. ## Installation The way to install `toise` and its depedencies is -with `conda`. If you do not already have `miniconda` on your system, obtain the -installer from https://conda.io/miniconda.html, and install in a location of -your choice, e.g.: +with [`micromamba`](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html). If you do not already have `micromamba` on your system, -```sh -sh ./Miniconda3-latest-Linux-x86_64.sh -p $CONDA_PREFIX +```console +"${SHELL}" <(curl -L micro.mamba.pm/install.sh) ``` -replacing `CONDA_PREFIX` with the prefix you chose. +or, os macOS with Homebrew: + +```console +brew install micromamba +``` -Then, obtain `toise`: +Next, obtain `toise`: ```sh git clone git@github.com:icecube/toise.git @@ -37,21 +39,9 @@ git clone git@github.com:icecube/toise.git Then, from the `toise` source directory, create a new environment: ```sh cd toise -$CONDA_PREFIX/bin/conda env create -n toise --file environment.yml -``` - -This will also download the required data tables. - -The above will install the latest available versions of all dependencies. You can also install exactly the versions that were most recently tested with: -```sh -cd toise - -PLATFORM_LOCKFILE=$(conda info --json | jq -r '"conda-\(.platform).lock"') -conda create -n toise --file $PLATFORM_LOCKFILE -cat $PLATFORM_LOCKFILE | awk '/^# pip/ {print substr($0,7)}' > requirements.txt -conda run -n toise pip install -r requirements.txt -e . +micromamba create -n toise --file conda-lock.yml +conda run -n toise pip install -e . ``` -This should be much faster, as it does not have to solve for compatible versions of all the dependencies. If you do not have `jq` installed, you can set `PLATFORM_LOCKFILE` by hand to e.g. `conda-osx-64.lock`. 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-https://conda.anaconda.org/conda-forge/noarch/tzdata-2021e-he74cb21_0.tar.bz2#a751ec502589ebdc2eceb183ff602569 -https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.2.5-pyh9f0ad1d_2.tar.bz2#5266fcd697043c59621fda522b3d78ee -https://conda.anaconda.org/conda-forge/noarch/wheel-0.37.0-pyhd8ed1ab_1.tar.bz2#3aa2c3e25dd361b453d010388b9cdff1 -https://conda.anaconda.org/conda-forge/noarch/zipp-3.6.0-pyhd8ed1ab_0.tar.bz2#855e2c4622f5eb50a4f6f7167b9ba17a -# pip easy-cache @ https://files.pythonhosted.org/packages/01/47/1d30783a8ce9df947f4d0c67726b3ecd0dfd22e363684b4eb1a8bf59e6e4/easy_cache-1.1.0-py3-none-any.whl#sha256=d99412159074d39891c83098dd5f0ca63bb56103e46efaa7e8455560680ce282 -# pip pydashi @ https://github.com/IceCube-SPNO/dashi/archive/refs/tags/v2.0.0-alpha.0.tar.gz -# pip pytest-pinned @ https://files.pythonhosted.org/packages/4a/08/98aad61bab14108d5dc6651d121994f955bd39fdd413bf8a2a2dc4d2ce7f/pytest_pinned-0.4.2-py3-none-any.whl#sha256=ebf8b6cd32772e940c20871f5c09ca35d18155390e649823b8435299a25bd88e diff --git a/conda-lock.yml b/conda-lock.yml index 571c538..4d4670f 100644 --- a/conda-lock.yml +++ b/conda-lock.yml @@ -1,24 +1,26 @@ -# This lock file was generated by conda-lock (https://github.com/conda-incubator/conda-lock). DO NOT EDIT! +# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT! # # A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike # e.g. `conda env create`, the resulting environment will not change as new package versions become # available, unless you explicitly update the lock file. # # Install this environment as "YOURENV" with: -# conda-lock install -n YOURENV --file conda-lock.yml +# conda-lock install -n YOURENV conda-lock.yml # This lock contains optional development dependencies. Include them in the installed environment with: -# conda-lock install --dev-dependencies -n YOURENV --file conda-lock.yml +# conda-lock install --dev-dependencies -n YOURENV conda-lock.yml # To update a single package to the latest version compatible with the version constraints in the source: -# conda-lock lock --lockfile conda-lock.yml --update PACKAGE +# conda-lock lock --lockfile conda-lock.yml --update PACKAGE # To re-solve the entire environment, e.g. after changing a version constraint in the source file: # conda-lock -f environment.yml -f dev-environment.yml --lockfile conda-lock.yml +version: 1 metadata: - channels: - - conda-forge content_hash: - linux-64: 13ebdcf8f949e9eb9f28381b24c35bb22c2b973b5e0c104ac3162438a88f4461 - osx-64: 2ddd5b82e77c56c492229b935e16dabe4c4f68bcb2ec2abb298133beac3b6719 - osx-arm64: f33ec806c688b70fbd1d29cad24483d1ae395a0124fc2fc9c2bca1705893e4ad + linux-64: a60006b65182c36afc3664df137bc30d196232a8ff5359d074ca9bd7b3ffea7f + osx-64: 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-https://conda.anaconda.org/conda-forge/osx-arm64/mpfr-4.1.0-h6d7a090_1.tar.bz2#c37f296f76cfb61d4f91613da93789e6 -https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.2-h9aa5885_4.tar.bz2#8a4aa25a5741e65f2338204f8a45d8d8 -https://conda.anaconda.org/conda-forge/osx-arm64/nuflux-2.0.2-py39hcc01ea5_1.tar.bz2#f738dcc325e56d02727e990cfead4e2f -https://conda.anaconda.org/conda-forge/osx-arm64/numexpr-2.7.3-py39h7f752ed_2.tar.bz2#96d593e80301a6827dfcbffa25dcfe6a -https://conda.anaconda.org/conda-forge/osx-arm64/numpy-1.21.4-py39h1f3b974_0.tar.bz2#ae8bfff0872f36c053ea4130818d7270 -https://conda.anaconda.org/conda-forge/osx-arm64/openjpeg-2.4.0-h062765e_1.tar.bz2#02ec6e9debe1bf6488ac302592d067fc -https://conda.anaconda.org/conda-forge/osx-arm64/openssl-3.0.0-h3422bc3_2.tar.bz2#a8c39e076c8d531dd9e73b7ff0dea96a -https://conda.anaconda.org/conda-forge/osx-arm64/pandas-1.3.4-py39h7f752ed_1.tar.bz2#72590755c6995e359cb031dd04e979cb -https://conda.anaconda.org/conda-forge/osx-arm64/photospline-2.0.7-py39hbfd55a9_0.tar.bz2#0457cf76605ad53e5593af484309f3f1 -https://conda.anaconda.org/conda-forge/osx-arm64/pillow-8.4.0-py39ha74c66e_0.tar.bz2#038dba961ccc2a21630d564ff48afc1d -https://conda.anaconda.org/conda-forge/osx-arm64/pluggy-1.0.0-py39h2804cbe_2.tar.bz2#636c947ba07c1582065f01453b6e4fef -https://conda.anaconda.org/conda-forge/osx-arm64/pydantic-1.8.2-py39h5161555_2.tar.bz2#f615f8c81fd4d403d124bc4601d7877b -https://conda.anaconda.org/conda-forge/osx-arm64/pyerfa-2.0.0.1-py39h20ef057_1.tar.bz2#d7c83deb0e2eda037e2c1a1aaa72af63 -https://conda.anaconda.org/conda-forge/osx-arm64/pyrsistent-0.18.0-py39h5161555_0.tar.bz2#f129a2eb1f8ca70fa5e7e3193d73dc28 -https://conda.anaconda.org/conda-forge/osx-arm64/pytables-3.6.1-py39h086b50d_4.tar.bz2#d73dc114f2d2d296e59bbbc1f5c99685 -https://conda.anaconda.org/conda-forge/osx-arm64/pytest-6.2.5-py39h2804cbe_1.tar.bz2#7f37779bafbefe9d1d32a2f5e17fc4fd -https://conda.anaconda.org/conda-forge/osx-arm64/python-3.9.7-hc0da0df_3_cpython.tar.bz2#4a9cb0347e7f1f5443ca7720cfd42cfb -https://conda.anaconda.org/conda-forge/osx-arm64/python_abi-3.9-2_cp39.tar.bz2#ba3082b5441b482d5cfe328d4e7ba0bf -https://conda.anaconda.org/conda-forge/osx-arm64/pyyaml-6.0-py39h5161555_3.tar.bz2#1169532ea0b9456d7ac8171807486614 -https://conda.anaconda.org/conda-forge/osx-arm64/pyzmq-22.3.0-py39h02c6a76_1.tar.bz2#8043c857734c4adef5a27ef8ab0ef8e8 -https://conda.anaconda.org/conda-forge/osx-arm64/readline-8.1-hedafd6a_0.tar.bz2#3ab98d5fd433cd392a1b0781391a9e38 -https://conda.anaconda.org/conda-forge/osx-arm64/scipy-1.7.2-py39h5060c3b_0.tar.bz2#754073c2b07bbb53f30a1dcc3621f505 -https://conda.anaconda.org/conda-forge/osx-arm64/setuptools-59.2.0-py39h2804cbe_0.tar.bz2#71789b9ebc713ccc0ebae4ce8e07bf71 -https://conda.anaconda.org/conda-forge/osx-arm64/sqlite-3.36.0-h72a2b83_2.tar.bz2#39b91d8b93b9950c166a6d27ea92f385 -https://conda.anaconda.org/conda-forge/osx-arm64/suitesparse-5.10.1-h7cd81ec_1.tar.bz2#aa2b4cd2c3c870a5da51032c97952e8e -https://conda.anaconda.org/conda-forge/osx-arm64/tbb-2021.4.0-hc021e02_1.tar.bz2#2abdcb4eb65a719eca9015c6d726cb8a -https://conda.anaconda.org/conda-forge/osx-arm64/tk-8.6.11-he1e0b03_1.tar.bz2#dd4c783060a6825a6e73a073c650be16 -https://conda.anaconda.org/conda-forge/osx-arm64/tornado-6.1-py39h5161555_2.tar.bz2#fffd4f597cb7b7cf8b7ff38ce3057635 -https://conda.anaconda.org/conda-forge/osx-arm64/xz-5.2.5-h642e427_1.tar.bz2#9ab2316785cb81c464ab9a99512dae71 -https://conda.anaconda.org/conda-forge/osx-arm64/yaml-0.2.5-h642e427_0.tar.bz2#143549bda61a8b9e3a223328cdddc811 -https://conda.anaconda.org/conda-forge/osx-arm64/zeromq-4.3.4-hbdafb3b_1.tar.bz2#49132c08da6545dc68351ff8b659ac8e -https://conda.anaconda.org/conda-forge/osx-arm64/zlib-1.2.11-hee7b306_1013.tar.bz2#0b65c3db409dd06257dd879605eddb45 -https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.0-h861e0a7_0.tar.bz2#3a3700f7735317734bf584b11a9475f6 -# pip easy-cache @ https://files.pythonhosted.org/packages/01/47/1d30783a8ce9df947f4d0c67726b3ecd0dfd22e363684b4eb1a8bf59e6e4/easy_cache-1.1.0-py3-none-any.whl#sha256=d99412159074d39891c83098dd5f0ca63bb56103e46efaa7e8455560680ce282 -# pip pydashi @ https://github.com/IceCube-SPNO/dashi/archive/refs/tags/v2.0.0-alpha.0.tar.gz -# pip pytest-pinned @ https://files.pythonhosted.org/packages/4a/08/98aad61bab14108d5dc6651d121994f955bd39fdd413bf8a2a2dc4d2ce7f/pytest_pinned-0.4.2-py3-none-any.whl#sha256=ebf8b6cd32772e940c20871f5c09ca35d18155390e649823b8435299a25bd88e diff --git a/environment.yml b/environment.yml index 7976ac9..6ca1162 100644 --- a/environment.yml +++ b/environment.yml @@ -6,7 +6,7 @@ platforms: - osx-64 - osx-arm64 dependencies: - - python >=3.8,<3.10 + - python >=3.8 - numpy - scipy>=0.15 - healpy @@ -22,6 +22,6 @@ dependencies: - photospline - pip - pip: - - easy-cache - - pydashi @ https://github.com/IceCube-SPNO/dashi/archive/refs/tags/v2.0.0-alpha.0.tar.gz#sha256=b2b8a179f4268d3619a72fc14f8f223f52bc9d51c3ff338863eb8b11c6bc0d5b + - easy-cache >=2 + - pydashi @ https://github.com/IceCube-SPNO/dashi/archive/refs/tags/v2.0.0.tar.gz#sha256=dde4d041e16d64e04e704f3f594c9158e3b0d6a5099fecf634a8b502e292d0bb - -e . diff --git a/toise/pointsource.py b/toise/pointsource.py index 2e063ae..93bde48 100644 --- a/toise/pointsource.py +++ b/toise/pointsource.py @@ -475,7 +475,7 @@ def f(flux_norm): ns = total - nb logging.getLogger().info( "baseline: %.2g actual %.2g ns: %.2g nb: %.2g ts: %.2g" - % (baseline, actual, ns, nb, ts(actual)) + % (baseline, actual[0], ns, nb, ts(actual)) ) return actual[0], ns, nb @@ -591,7 +591,7 @@ def f(flux_norm): else: # actual = optimize.bisect(f, 0, baseline, xtol=baseline*1e-2) actual = optimize.fsolve(f, baseline, xtol=tolerance, factor=1, epsfcn=1) - logging.getLogger().debug("baseline: %.2g actual %.2g" % (baseline, actual)) + logging.getLogger().debug("baseline: %.2g actual %.2g" % (baseline, actual[0])) allh = asimov_llh(components, ps=actual, **fixed) total = nevents(allh, ps=actual, **fixed) nb = nevents(allh, ps=0, **fixed)