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Added testing for namespace module support
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| Original file line number | Diff line number | Diff line change |
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| # This file must exist with these contents | ||
| from .stage import PipelineStage | ||
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| if __name__ == "__main__": | ||
| PipelineStage.main() |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,215 @@ | ||
| from ceci import PipelineStage | ||
| from ceci_example.types import TextFile, YamlFile | ||
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| class NMshearMeasurementPipe(PipelineStage): | ||
| """ | ||
| This pipeline element is a template for a shape measurement tool | ||
| """ | ||
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| name = "NMshearMeasurementPipe" | ||
| inputs = [("DM", TextFile)] | ||
| outputs = [("shear_catalog", TextFile)] | ||
| config_options = {"metacalibration": bool, "apply_flag": bool} | ||
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| def run(self): | ||
| # Retrieve configuration: | ||
| my_config = self.config | ||
| print("Here is my configuration :", my_config) | ||
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| for inp, _ in self.inputs: | ||
| filename = self.get_input(inp) | ||
| print(f" shearMeasurementPipe reading from {filename}") | ||
| open(filename) | ||
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| for out, _ in self.outputs: | ||
| filename = self.get_output(out) | ||
| print(f" shearMeasurementPipe writing to {filename}") | ||
| open(filename, "w").write("shearMeasurementPipe was here \n") | ||
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| class NMPZEstimationPipe(PipelineStage): | ||
| name = "NMPZEstimationPipe" | ||
| inputs = [("DM", TextFile), ("fiducial_cosmology", TextFile)] | ||
| outputs = [("photoz_pdfs", TextFile)] | ||
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| def run(self): | ||
| for inp, _ in self.inputs: | ||
| filename = self.get_input(inp) | ||
| print(f" PZEstimationPipe reading from {filename}") | ||
| open(filename) | ||
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| for out, _ in self.outputs: | ||
| filename = self.get_output(out) | ||
| print(f" PZEstimationPipe writing to {filename}") | ||
| open(filename, "w").write("PZEstimationPipe was here \n") | ||
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| class NMWLGCRandoms(PipelineStage): | ||
| name = "NMWLGCRandoms" | ||
| inputs = [("diagnostic_maps", TextFile)] | ||
| outputs = [("random_catalog", TextFile)] | ||
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| def run(self): | ||
| for inp, _ in self.inputs: | ||
| filename = self.get_input(inp) | ||
| print(f" WLGCRandoms reading from {filename}") | ||
| open(filename) | ||
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| for out, _ in self.outputs: | ||
| filename = self.get_output(out) | ||
| print(f" WLGCRandoms writing to {filename}") | ||
| open(filename, "w").write("WLGCRandoms was here \n") | ||
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| class NMWLGCSelector(PipelineStage): | ||
| name = "NMWLGCSelector" | ||
| inputs = [("shear_catalog", TextFile), ("photoz_pdfs", TextFile)] | ||
| outputs = [("tomography_catalog", TextFile)] | ||
| config_options = {"zbin_edges": [float], "ra_range": [-5.0, 5.0]} | ||
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| def run(self): | ||
| print(self.config) | ||
| for inp, _ in self.inputs: | ||
| filename = self.get_input(inp) | ||
| print(f" WLGCSelector reading from {filename}") | ||
| open(filename) | ||
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| for out, _ in self.outputs: | ||
| filename = self.get_output(out) | ||
| print(f" WLGCSelector writing to {filename}") | ||
| open(filename, "w").write("WLGCSelector was here \n") | ||
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| class NMSourceSummarizer(PipelineStage): | ||
| name = "NMSourceSummarizer" | ||
| inputs = [ | ||
| ("tomography_catalog", TextFile), | ||
| ("photoz_pdfs", TextFile), | ||
| ("diagnostic_maps", TextFile), | ||
| ] | ||
| outputs = [("source_summary_data", TextFile)] | ||
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| def run(self): | ||
| for inp, _ in self.inputs: | ||
| filename = self.get_input(inp) | ||
| print(f" SourceSummarizer reading from {filename}") | ||
| open(filename) | ||
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| for out, _ in self.outputs: | ||
| filename = self.get_output(out) | ||
| print(f" SourceSummarizer writing to {filename}") | ||
| open(filename, "w").write("SourceSummarizer was here \n") | ||
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| class NMSysMapMaker(PipelineStage): | ||
| name = "NMSysMapMaker" | ||
| inputs = [("DM", TextFile)] | ||
| outputs = [("diagnostic_maps", TextFile)] | ||
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| def run(self): | ||
| for inp, _ in self.inputs: | ||
| filename = self.get_input(inp) | ||
| print(f" SysMapMaker reading from {filename}") | ||
| open(filename) | ||
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| for out, _ in self.outputs: | ||
| filename = self.get_output(out) | ||
| print(f" SysMapMaker writing to {filename}") | ||
| open(filename, "w").write("SysMapMaker was here \n") | ||
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| class NMWLGCTwoPoint(PipelineStage): | ||
| name = "NMWLGCTwoPoint" | ||
| inputs = [ | ||
| ("tomography_catalog", TextFile), | ||
| ("shear_catalog", TextFile), | ||
| ("diagnostic_maps", TextFile), | ||
| ("random_catalog", TextFile), | ||
| ] | ||
| outputs = [("twopoint_data", TextFile)] | ||
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| def run(self): | ||
| for inp, _ in self.inputs: | ||
| filename = self.get_input(inp) | ||
| print(f" WLGCTwoPoint reading from {filename}") | ||
| open(filename) | ||
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| for out, _ in self.outputs: | ||
| filename = self.get_output(out) | ||
| print(f" WLGCTwoPoint writing to {filename}") | ||
| open(filename, "w").write("WLGCTwoPoint was here \n") | ||
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| class NMWLGCCov(PipelineStage): | ||
| name = "NMWLGCCov" | ||
| inputs = [ | ||
| ("fiducial_cosmology", TextFile), | ||
| ("tomography_catalog", TextFile), | ||
| ("shear_catalog", TextFile), | ||
| ("source_summary_data", TextFile), | ||
| ("diagnostic_maps", TextFile), | ||
| ] | ||
| outputs = [("covariance", TextFile)] | ||
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| def rank_filename(self, rank, size): | ||
| filename = self.get_output("covariance") | ||
| if size == 1: | ||
| fname = filename | ||
| else: | ||
| fname = f"{filename}.{rank}" | ||
| return fname | ||
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| def run(self): | ||
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| # MPI Information | ||
| rank = self.rank | ||
| size = self.size | ||
| comm = self.comm | ||
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| for inp, _ in self.inputs: | ||
| filename = self.get_input(inp) | ||
| print(f" WLGCCov rank {rank}/{size} reading from {filename}") | ||
| open(filename) | ||
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| filename = self.get_output("covariance") | ||
| my_filename = self.rank_filename(rank, size) | ||
| print(f" WLGCCov rank {rank}/{size} writing to {my_filename}") | ||
| open(my_filename, "w").write(f"WLGCCov rank {rank} was here \n") | ||
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| # | ||
| if comm: | ||
| comm.Barrier() | ||
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| # If needed, concatenate all files | ||
| if rank == 0 and size > 1: | ||
| f = open(filename, "w") | ||
| print(f"Master process concatenating files:") | ||
| for i in range(size): | ||
| fname = self.rank_filename(i, size) | ||
| print(f" {fname}") | ||
| content = open(fname).read() | ||
| f.write(content) | ||
| f.close() | ||
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| class NMWLGCSummaryStatistic(PipelineStage): | ||
| name = "NMWLGCSummaryStatistic" | ||
| inputs = [ | ||
| ("twopoint_data", TextFile), | ||
| ("covariance", TextFile), | ||
| ("source_summary_data", TextFile), | ||
| ] | ||
| outputs = [("wlgc_summary_data", TextFile)] | ||
| parallel = False | ||
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| def run(self): | ||
| for inp, _ in self.inputs: | ||
| filename = self.get_input(inp) | ||
| print(f" WLGCSummaryStatistic reading from {filename}") | ||
| open(filename) | ||
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| for out, _ in self.outputs: | ||
| filename = self.get_output(out) | ||
| print(f" WLGCSummaryStatistic writing to {filename}") | ||
| open(filename, "w").write("WLGCSummaryStatistic was here \n") |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| python -m pytest --cov=./ceci --cov-report=html tests | ||
| python -m pytest --cov=./ceci --cov-branch --cov-report=html tests |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| global: | ||
| metacalibration: True | ||
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| NMshearMeasurementPipe: | ||
| apply_flag: False | ||
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| NMWLGCSelector: | ||
| zbin_edges: [0.2, 0.3, 0.5] | ||
| ra_range: [-5, 5] |
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