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Merge pull request #250 from LSSTDESC/issue/238/reorganize
Issue/238/reorganize
2 parents 3bb255c + 69b4c8b commit a704fce

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‎docs/conf.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -199,7 +199,7 @@ def run_apidoc(_):
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from sphinx.ext.apidoc import main as apidoc_main
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cur_dir = os.path.normpath(os.path.dirname(__file__))
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output_path = os.path.join(cur_dir, 'api')
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modules = os.path.normpath(os.path.join(cur_dir, "../rail"))
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modules = os.path.normpath(os.path.join(cur_dir, "../src/rail"))
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paramlist = ['--separate', '--implicit-namespaces', '--no-toc', '-f', '-M', '-o', output_path, modules]
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apidoc_main(paramlist)
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‎examples/core/FileIO_DataStore.ipynb

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@@ -54,8 +54,8 @@
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"outputs": [],
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"source": [
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"from rail.core.utils import RAILDIR\n",
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"trainFile = os.path.join(RAILDIR, 'tests/data/test_dc2_training_9816.hdf5')\n",
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"testFile = os.path.join(RAILDIR, 'tests/data/test_dc2_validation_9816.hdf5')\n",
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"trainFile = os.path.join(RAILDIR, 'rail/examples/testdata/test_dc2_training_9816.hdf5')\n",
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"testFile = os.path.join(RAILDIR, 'rail/examples/testdata/test_dc2_validation_9816.hdf5')\n",
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"\n",
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"traindata_io = tables_io.read(trainFile)[\"photometry\"]"
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]
@@ -386,7 +386,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.12"
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"version": "3.9.7"
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}
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},
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"nbformat": 4,

‎examples/core/Pipe_Example.ipynb

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@@ -75,7 +75,7 @@
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"outputs": [],
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"source": [
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"from rail.core.utils import RAILDIR\n",
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"flow_file = os.path.join(RAILDIR, 'examples/goldenspike/data/pretrained_flow.pkl')\n",
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"flow_file = os.path.join(RAILDIR, 'rail/examples/goldenspike/data/pretrained_flow.pkl')\n",
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"bands = ['u','g','r','i','z','y']\n",
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"band_dict = {band:f'mag_{band}_lsst' for band in bands}\n",
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"rename_dict = {f'mag_{band}_lsst_err':f'mag_err_{band}_lsst' for band in bands}\n",
@@ -317,7 +317,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.12"
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"version": "3.9.7"
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}
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},
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"nbformat": 4,

‎examples/core/hyperbolic_magnitude_test.ipynb

+2-2
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@@ -67,7 +67,7 @@
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"outputs": [],
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"source": [
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"from rail.core.utils import RAILDIR\n",
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"testFile = os.path.join(RAILDIR, 'tests', 'data', 'test_dc2_training_9816.pq')\n",
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"testFile = os.path.join(RAILDIR, 'rail', 'examples', 'testdata', 'test_dc2_training_9816.pq')\n",
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"test_mags = DS.read_file(\"test_data\", TableHandle, testFile)"
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]
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},
@@ -228,7 +228,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.12"
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"version": "3.9.7"
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}
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},
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"nbformat": 4,

‎examples/core/iterator_test.ipynb

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@@ -69,7 +69,7 @@
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"outputs": [],
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"source": [
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"from rail.core.utils import RAILDIR\n",
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"pdfs_file = os.path.join(RAILDIR, \"tests/data/test_dc2_training_9816.hdf5\")"
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"pdfs_file = os.path.join(RAILDIR, \"rail/examples/testdata/test_dc2_training_9816.hdf5\")"
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]
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},
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{
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.12"
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"version": "3.9.7"
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}
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},
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"nbformat": 4,

‎examples/estimation/NZDir.ipynb

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@@ -78,8 +78,8 @@
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"outputs": [],
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"source": [
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"from rail.core.utils import RAILDIR\n",
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"trainFile = os.path.join(RAILDIR, 'tests/data/test_dc2_training_9816.hdf5')\n",
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"testFile = os.path.join(RAILDIR, 'tests/data/test_dc2_validation_9816.hdf5')\n",
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"trainFile = os.path.join(RAILDIR, 'rail/examples/testdata/test_dc2_training_9816.hdf5')\n",
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"testFile = os.path.join(RAILDIR, 'rail/examples/testdata/test_dc2_validation_9816.hdf5')\n",
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"training_data = DS.read_file(\"training_data\", TableHandle, trainFile)"
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]
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},
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"display_name": "mvrail",
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"language": "python",
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"name": "python3"
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"name": "mvrail"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.12"
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"version": "3.9.13"
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}
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},
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"nbformat": 4,

‎examples/estimation/RAIL_estimation_demo.ipynb

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@@ -161,8 +161,8 @@
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"outputs": [],
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"source": [
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"from rail.core.utils import RAILDIR\n",
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"trainFile = os.path.join(RAILDIR, 'tests/data/test_dc2_training_9816.hdf5')\n",
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"testFile = os.path.join(RAILDIR, 'tests/data/test_dc2_validation_9816.hdf5')\n",
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"trainFile = os.path.join(RAILDIR, 'rail/examples/testdata/test_dc2_training_9816.hdf5')\n",
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"testFile = os.path.join(RAILDIR, 'rail/examples/testdata/test_dc2_validation_9816.hdf5')\n",
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"training_data = DS.read_file(\"training_data\", TableHandle, trainFile)\n",
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"test_data = DS.read_file(\"test_data\", TableHandle, testFile)"
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]
@@ -506,9 +506,9 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"display_name": "mvrail",
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"language": "python",
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"name": "python3"
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"name": "mvrail"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.12"
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"version": "3.9.13"
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}
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},
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"nbformat": 4,

‎examples/estimation/SimpleSOM_demo.ipynb

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@@ -683,9 +683,9 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"display_name": "mvrail",
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"language": "python",
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"name": "python3"
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"name": "mvrail"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.7"
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"version": "3.9.13"
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}
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},
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"nbformat": 4,

‎examples/estimation/test_sampled_summarizers.ipynb

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‎examples/evaluation/demo.ipynb

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@@ -85,11 +85,11 @@
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"### Photo-z Results\n",
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"#### Run FZBoost\n",
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"\n",
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"Go to dir `<your_path>/RAIL/examples/estimation/` and run the notebook `RAIL_estimation_demo.ipynb`, this will produce a file `output_fzboost.fits`\n",
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"Go to dir `<your_path>/RAIL/examples/estimation/` (i.e. \"../estimation\" relative to the directory you are running this notebook) and run the notebook `RAIL_estimation_demo.ipynb`, this will produce a file `output_fzboost.fits`\n",
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"\n",
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"writen at the location:<br> \n",
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"`<your_path>/RAIL/examples/estimation/output_fzboost.fits`. \n",
92-
"This will read in the FZBoost PDF results as a qp Ensemble.\n"
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"This will run FZBoost and write out the PDF results as a qp Ensemble that we will then use in this example notebook.\n"
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]
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},
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{
@@ -106,8 +106,8 @@
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"outputs": [],
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"source": [
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"from rail.core.utils import RAILDIR\n",
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"pdfs_file = os.path.join(RAILDIR, \"examples/estimation/output_fzboost.hdf5\")\n",
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"ztrue_file = os.path.join(RAILDIR, \"tests/data/test_dc2_validation_9816.hdf5\")"
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"pdfs_file = \"../estimation/output_fzboost.hdf5\"\n",
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"ztrue_file = os.path.join(RAILDIR, 'rail/examples/testdata/test_dc2_validation_9816.hdf5')"
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]
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},
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{
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.12"
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"version": "3.9.7"
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}
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},
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"nbformat": 4,

‎examples/goldenspike/goldenspike.ipynb

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],
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"metadata": {
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"kernelspec": {
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"display_name": "testcreation",
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"display_name": "mvrail",
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"language": "python",
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"name": "testcreation"
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"name": "mvrail"
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},
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"language_info": {
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"codemirror_mode": {

‎pyproject.toml

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1+
[project]
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name = "pz-rail"
3+
description = "Redshift Assessment Infrastructure Layers"
4+
readme = "README.rst"
5+
requires-python = ">=3.8"
6+
license = { file = "LICENSE" }
7+
authors = [
8+
{ name = "The LSST DESC PZ WG", email = "[email protected]" }
9+
]
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classifiers = [
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"Development Status :: 4 - Beta",
12+
"License :: OSI Approved :: MIT License",
13+
"Intended Audience :: Developers",
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"Intended Audience :: Science/Research",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.10",
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"Natural Language :: English",
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"Operating System :: POSIX"
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]
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dynamic = ["version"]
22+
dependencies = [
23+
"h5py",
24+
"numpy",
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"pandas>=1.1",
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"tables-io>=0.7.5",
27+
"ceci>=1.10.1",
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"pyyaml",
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"minisom",
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"scipy>=1.9.0",
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"pz-hyperbolic-temp",
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"qp-prob",
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"sklearn",
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"pzflow",
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]
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[project.optional-dependencies]
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dev = [
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"coverage",
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"pylint",
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"pytest",
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"pytest-cov",
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"yamllint",
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]
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[build-system]
47+
requires = ["setuptools>=61", "wheel", "setuptools_scm[toml]>=6.2"]
48+
build-backend = "setuptools.build_meta"
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[tool.setuptools_scm]
51+
write_to = "src/rail/core/_version.py"
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[tool.setuptools.package-data]
54+
"rail.examples.estimation.data.AB" = ["*.txt"]
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"rail.examples.estimation.data.FILTER" = ["*.res"]
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"rail.examples.estimation.data.SED" = ["*.sed", "*.list"]
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"rail.examples.estimation" = ["*.pkl"]
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"rail.examples.creation.configs" = ["*.yaml"]
59+
"rail.examples.creation.data" = ["*.pkl", "*.hdf5"]
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"rail.examples.creation.success_rate_data" = ["*.txt"]
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"rail.examples.goldenspike" = ["*.yaml"]
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"rail.examples.goldenspike.data" = ["*.pkl", "*.pq"]
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"rail.examples.testdata" = ["*.ipynb", "*.fits", "*.hdf5", "*.pq", "*.md"]
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[tool.coverage.run]
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source = ["src/rail"]
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branch = false
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[tool.coverage.report]
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show_missing = true
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exclude_lines = [
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"pragma: no cover",
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"def __repr__",
74+
"if self.debug:",
75+
"if settings.DEBUG",
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"raise AssertionError",
77+
"raise NotImplementedError",
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"if 0:",
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"if __name__ == .__main__.:",
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"if TYPE_CHECKING:"
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]
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[tool.black]
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line-length = 110
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target-version = ["py310"]
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[tool.pydocstyle]
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convention = "numpy"
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add_select = [
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"D212" # Multi-line docstring summary should start at the first line
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]
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add-ignore = [
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"D105", # Missing docstring in magic method
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"D102", # Missing docstring in public method (needed for docstring inheritance)
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"D100", # Missing docstring in public module
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# Below are required to allow multi-line summaries.
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"D200", # One-line docstring should fit on one line with quotes
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"D205", # 1 blank line required between summary line and description
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"D400", # First line should end with a period
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# Properties shouldn't be written in imperative mode. This will be fixed
101+
# post 6.1.1, see https://github.com/PyCQA/pydocstyle/pull/546
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"D401",
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]
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[tool.pylint]
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disable = [
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"abstract-method",
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"invalid-name",
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"too-many-statements",
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"missing-module-docstring",
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"missing-class-docstring",
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"missing-function-docstring",
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"too-few-public-methods",
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"duplicate-code"
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]
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max-line-length = 110
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max-locals = 50
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max-branches = 25
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max-public-methods = 50
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[tool.isort]
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profile = "black"
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line_length = 110
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[tool.pytest.ini_options]
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addopts = [
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"--cov=rail",
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"--cov-report=html"
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]
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flake8-ignore = "E203"
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[tool.mypy]
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disallow_untyped_defs = true
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disallow_incomplete_defs = true
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ignore_missing_imports = true
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namespace_packages = true
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plugins = "sqlalchemy.ext.mypy.plugin"
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show_error_codes = true
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strict_equality = true
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warn_redundant_casts = true
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warn_unreachable = true
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warn_unused_ignores = true

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