Minimal pip packaging (#4)

* added error message on no data file * added install script * removed orphics dependency * allowed changing of data dir * added pyproject from flit * added gitignore * update gitignore to boilerplate * corrected data dir global use * added pandas req * remove pandas dep (oops) * ver bump * requirements again * deps still weird * version and url * direct people to orphics
ACTCollaboration · Aug 18, 2023 · 4aa5e94 · 4aa5e94
1 parent 5df396c
commit 4aa5e94
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Showing 6 changed files with 106 additions and 7 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,52 @@
+**/.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+# Sphinx documentation
+docs/_build/
diff --git a/act_dr6_lenslike/__init__.py b/act_dr6_lenslike/__init__.py
@@ -1,3 +1,4 @@
+"""Likelihood for the Atacama Cosmology Telescope DR6 CMB lensing data."""
 __author__ = "Mathew Madhavacheril"
 __version__ = "1.0.0"
 

diff --git a/act_dr6_lenslike/act_dr6_lenslike.py b/act_dr6_lenslike/act_dr6_lenslike.py
@@ -135,7 +135,6 @@ def parse_variant(variant):
     include_planck = True if 'actplanck' in variant else False
     return v,baseline,include_planck
 
-
 # ==================            
 # Generic likelihood
 # ==================
@@ -153,7 +152,8 @@ def parse_variant(variant):
 chi_square = -2 lnlike
 """
 
-def load_data(variant,lens_only=False,
+def load_data(variant, ddir=data_dir,
+              lens_only=False,
               apply_hartlap=True,like_corrections=True,mock=False,
               nsims_act=796,nsims_planck=400,trim_lmax=2998,scale_cov=None):
     """
@@ -191,13 +191,13 @@ def load_data(variant,lens_only=False,
 
     # Fiducial spectra
     if like_corrections:
-        f_ls, f_tt, f_ee, f_bb, f_te = np.loadtxt(f"{data_dir}/like_corrs/cosmo2017_10K_acc3_lensedCls.dat",unpack=True)
+        f_ls, f_tt, f_ee, f_bb, f_te = np.loadtxt(f"{ddir}/like_corrs/cosmo2017_10K_acc3_lensedCls.dat",unpack=True)
         f_tt = f_tt / (f_ls * (f_ls+1.)) * 2. * np.pi
         f_ee = f_ee / (f_ls * (f_ls+1.)) * 2. * np.pi
         f_bb = f_bb / (f_ls * (f_ls+1.)) * 2. * np.pi
         f_te = f_te / (f_ls * (f_ls+1.)) * 2. * np.pi
 
-        fd_ls, f_dd = np.loadtxt(f"{data_dir}/like_corrs/cosmo2017_10K_acc3_lenspotentialCls.dat",unpack=True,usecols=[0,5])
+        fd_ls, f_dd = np.loadtxt(f"{ddir}/like_corrs/cosmo2017_10K_acc3_lenspotentialCls.dat",unpack=True,usecols=[0,5])
         f_kk = f_dd * 2. * np.pi / 4.
         d['fiducial_cl_tt'] = standardize(f_ls,f_tt,trim_lmax)
         d['fiducial_cl_te'] = standardize(f_ls,f_te,trim_lmax)
@@ -207,7 +207,6 @@ def load_data(variant,lens_only=False,
 
 
     # Return data bandpowers, covariance matrix and binning matrix
-    ddir = data_dir
     if baseline:
         start = 2
         end = -6
@@ -369,7 +368,11 @@ class GenericLimberCosmicShear(InstallableLikelihood):
     cmb_noise = None
 
     def initialize(self):
-        from orphics import stats
+        try:
+            from orphics import stats
+        except ImportError:
+            print("Error importing orphics library. Please install.\n\
+                  available at https://github.com/msyriac/orphics")
         import pyfisher
         bin_edges = np.geomspace(self.glmin,self.lmax,self.nell)
         bin_edges = bin_edges[bin_edges>self.lmin]

diff --git a/act_dr6_lenslike/tests/test_act.py b/act_dr6_lenslike/tests/test_act.py
@@ -5,10 +5,19 @@
 data_dir = alike.data_dir
 
 
+
 class ACTLikeTest(unittest.TestCase):
 
     def generic_call(self,variant,lens_only,exp_chisq=None):
-        ell, cl_tt, cl_ee, cl_bb, cl_te, cl_pp, cl_tp, cl_ep= np.loadtxt(data_dir+'like_corrs/cosmo2017_10K_acc3_lenspotentialCls.dat', unpack=True)
+        data_file = data_dir+'like_corrs/cosmo2017_10K_acc3_lenspotentialCls.dat'
+        try:
+            ell, cl_tt, cl_ee, cl_bb, cl_te, cl_pp, cl_tp, cl_ep= np.loadtxt(data_file, unpack=True)
+        except OSError:
+            raise
+        finally:
+            print('Required data file not found at {}'.format(data_file))
+            print('Please obtain it and place it correctly.')
+            print('The script get-act-data.sh will download and place it.')
         prefac = 2*np.pi/ell/(ell+1.)
         cl_kk=cl_pp/4*2*np.pi
         cl_bb = cl_bb*prefac

diff --git a/get-act-data.sh b/get-act-data.sh
@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+
+# script from Joe Zuntz
+
+if [ -d act_dr6_lenslike/data/v1.1 ]
+then
+    echo ACT DR6 Lensing data already downloaded
+elif ! command -v wget &> /dev/null
+then
+    echo wget not installed. Please obtain it \(e.g. conda install wget\) to download the data.
+else
+    mkdir -p act_dr6_lenslike/data
+    pushd act_dr6_lenslike/data
+    wget https://lambda.gsfc.nasa.gov/data/suborbital/ACT/ACT_dr6/likelihood/data/ACT_dr6_likelihood_v1.1.tgz
+    tar -zxvf ACT_dr6_likelihood_v1.1.tgz
+    rm ACT_dr6_likelihood_v1.1.tgz
+    popd
+fi
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,16 @@
+[build-system]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "act_dr6_lenslike"
+authors = [{name = "Mathew Madhavacheril", email = "[email protected]"}]
+readme = "README.md"
+classifiers = [
+	"License :: OSI Approved :: BSD License",
+]
+dynamic = ["version", "description"]
+dependencies = ["numpy >=1", "scipy >=1"]
+
+[project.urls]
+Source = "https://github.com/ACTCollaboration/act_dr6_lenslike"