Adapt workflow to use config.path_data and config.path_results

adonath · Oct 17, 2023 · 9d19aad · 9d19aad
1 parent 2a455f6
commit 9d19aad
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Showing 14 changed files with 40 additions and 38 deletions.
diff --git a/config/config.yaml b/config/config.yaml
@@ -1,7 +1,7 @@
 name: my-config
 scfile: data/L231017092559388FF7BE86_SC00.fits
-data_path: data/
-result_path: results/
+path_data: data/
+path_results: results/
 event_types: ["psf0", "psf1", "psf2", "psf3"]
 fermitools:
   gtselect:

diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -271,6 +271,8 @@ class FermiToolsConfig(BaseConfig):
 class SnakeMakeFermiLATConfig(BaseConfig):
     name: str = "my-config"
     scfile: str
+    path_data: str = "data"
+    path_results: str = "results"
     event_types: List[EventTypeEnum] = ["FRONT", "BACK"]
     ltcube: Optional[str] = None
     fermitools = FermiToolsConfig = FermiToolsConfig()
@@ -304,8 +306,8 @@ include: "rules/summarize-gp-spectra.smk"
 # all rule 
 rule all:
     input:
-        expand("results/{config_name}/datasets/{config_name}-{event_type}-dataset.fits", config_name=config_obj.name, event_type=config_obj.event_types),
-        expand("results/{config_name}/datasets/{config_name}-datasets-all.yaml", config_name=config_obj.name),
-        expand("results/{config_name}/model/{config_name}-model.yaml", config_name=config_obj.name),
-        expand("results/{config_name}/summary/images/{event_type}/{config_name}-{event_type}-counts-image.png", config_name=config_obj.name, event_type=config_obj.event_types),
-        expand("results/{config_name}/summary/images/{config_name}-counts-spectra.png", config_name=config_obj.name),
+        expand("config[path_results]/{config_name}/datasets/{config_name}-{event_type}-dataset.fits", config_name=config_obj.name, event_type=config_obj.event_types),
+        expand("config[path_results]/{config_name}/datasets/{config_name}-datasets-all.yaml", config_name=config_obj.name),
+        expand("config[path_results]/{config_name}/model/{config_name}-model.yaml", config_name=config_obj.name),
+        expand("config[path_results]/{config_name}/summary/images/{event_type}/{config_name}-{event_type}-counts-image.png", config_name=config_obj.name, event_type=config_obj.event_types),
+        expand("config[path_results]/{config_name}/summary/images/{config_name}-counts-spectra.png", config_name=config_obj.name),
diff --git a/workflow/rules/gather.smk b/workflow/rules/gather.smk
@@ -1,5 +1,5 @@
 rule gather_event_files:
     output:
-        "results/events.txt"
+        "{config[path_results]}/events.txt"
     shell: 
-        "ls data/*_PH* > {output}"
+        "ls {config[path_data]}/*_PH* > {output}"
diff --git a/workflow/rules/gtbin.smk b/workflow/rules/gtbin.smk
@@ -1,8 +1,8 @@
 rule gtbin:
     input:
-        "results/{config_name}/events/filtered/{config_name}-{event_type}-events-selected-filtered.fits"
+        "config[path_results]/{config_name}/events/filtered/{config_name}-{event_type}-events-selected-filtered.fits"
     output:
-        "results/{config_name}/maps/{event_type}/{config_name}-{event_type}-counts.fits"
+        "config[path_results]/{config_name}/maps/{event_type}/{config_name}-{event_type}-counts.fits"
     log: "logs/{config_name}/{event_type}/gtbin.log"
     run:
         args = gtbin.to_cmd_args()

diff --git a/workflow/rules/gtexpcube2.smk b/workflow/rules/gtexpcube2.smk
@@ -1,8 +1,8 @@
 rule gtexpcube2:
     input:
-        "results/{config_name}/{config_name}-ltcube.fits"
+        "config[path_results]/{config_name}/{config_name}-ltcube.fits"
     output:
-        "results/{config_name}/maps/{event_type}/{config_name}-{event_type}-exposure.fits"
+        "config[path_results]/{config_name}/maps/{event_type}/{config_name}-{event_type}-exposure.fits"
     log:
         "logs/{config_name}/{event_type}/gtexpcube2.log"
     run:

diff --git a/workflow/rules/gtltcube.smk b/workflow/rules/gtltcube.smk
@@ -1,8 +1,8 @@
 rule gtltcube:
     input:
-       expand("results/{config_name}/events/filtered/{config_name}-{event_type}-events-selected-filtered.fits", config_name=config["name"], event_type=config_obj.event_types)
+       expand("config[path_results]/{config_name}/events/filtered/{config_name}-{event_type}-events-selected-filtered.fits", config_name=config["name"], event_type=config_obj.event_types)
     output:
-        "results/{config_name}/{config_name}-ltcube.fits"
+        "config[path_results]/{config_name}/{config_name}-ltcube.fits"
     log:
         "logs/{config_name}/gtltcube.log"
     run:

diff --git a/workflow/rules/gtmktime.smk b/workflow/rules/gtmktime.smk
@@ -1,8 +1,8 @@
 rule gtmktime:
     input:
-        "results/{config_name}/events/{config_name}-{event_type}-events-selected.fits"
+        "config[path_results]/{config_name}/events/{config_name}-{event_type}-events-selected.fits"
     output:
-        "results/{config_name}/events/filtered/{config_name}-{event_type}-events-selected-filtered.fits"
+        "config[path_results]/{config_name}/events/filtered/{config_name}-{event_type}-events-selected-filtered.fits"
     log:
         "logs/{config_name}/{event_type}/gtmktime.log"
     run:

diff --git a/workflow/rules/gtpsf.smk b/workflow/rules/gtpsf.smk
@@ -1,8 +1,8 @@
 rule gtpsf:
     input:
-        "results/{config_name}/{config_name}-ltcube.fits"
+        "config[path_results]/{config_name}/{config_name}-ltcube.fits"
     output:
-        "results/{config_name}/maps/{event_type}/{config_name}-{event_type}-psf.fits"
+        "config[path_results]/{config_name}/maps/{event_type}/{config_name}-{event_type}-psf.fits"
     log:
         "logs/{config_name}/{event_type}/gtpsf.log"
     run:

diff --git a/workflow/rules/gtselect.smk b/workflow/rules/gtselect.smk
@@ -1,8 +1,8 @@
 rule gtselect:
     input:
-        "results/events.txt"
+        "config[path_results]/events.txt"
     output:
-        "results/{config_name}/events/{config_name}-{event_type}-events-selected.fits"
+        "config[path_results]/{config_name}/events/{config_name}-{event_type}-events-selected.fits"
     log:
         "logs/{config_name}/{event_type}/gtselect.log"
     run: 

diff --git a/workflow/rules/prepare-gp-dataset.smk b/workflow/rules/prepare-gp-dataset.smk
@@ -1,10 +1,10 @@
 rule prepare_gp_dataset:
     input:
-        "results/{config_name}/maps/{event_type}/{config_name}-{event_type}-counts.fits",
-        "results/{config_name}/maps/{event_type}/{config_name}-{event_type}-exposure.fits",
-        "results/{config_name}/maps/{event_type}/{config_name}-{event_type}-psf.fits",
+        "config[path_results]/{config_name}/maps/{event_type}/{config_name}-{event_type}-counts.fits",
+        "config[path_results]/{config_name}/maps/{event_type}/{config_name}-{event_type}-exposure.fits",
+        "config[path_results]/{config_name}/maps/{event_type}/{config_name}-{event_type}-psf.fits",
     output:
-        "results/{config_name}/datasets/{config_name}-{event_type}-dataset.fits",
+        "config[path_results]/{config_name}/datasets/{config_name}-{event_type}-dataset.fits",
     log:
         "logs/{config_name}/{event_type}/prepare-gp-dataset.log"
     run:

diff --git a/workflow/rules/prepare-gp-datasets-yaml.smk b/workflow/rules/prepare-gp-datasets-yaml.smk
@@ -1,8 +1,8 @@
 rule prepare_gp_datasets_yaml:
     input:
-        expand("results/{config_name}/datasets/{config_name}-{event_type}-dataset.fits", config_name=config["name"], event_type=config_obj.event_types)
+        expand("config[path_results]/{config_name}/datasets/{config_name}-{event_type}-dataset.fits", config_name=config["name"], event_type=config_obj.event_types)
     output:
-        "results/{config_name}/datasets/{config_name}-datasets-all.yaml"
+        "config[path_results]/{config_name}/datasets/{config_name}-datasets-all.yaml"
     log:
         "logs/{config_name}/prepare-gp-datasets-yaml.log"
     run:

diff --git a/workflow/rules/prepare-gp-model.smk b/workflow/rules/prepare-gp-model.smk
@@ -1,7 +1,7 @@
 rule prepare_gp_model:
     output:
-        "results/{config_name}/model/{config_name}-model.yaml",
-        "results/{config_name}/model/{config_name}-galactic-diffuse-model.fits",
+        "config[path_results]/{config_name}/model/{config_name}-model.yaml",
+        "config[path_results]/{config_name}/model/{config_name}-galactic-diffuse-model.fits",
     log:
         "logs/{config_name}/prepare-gp-model.log"
     run:

diff --git a/workflow/rules/summarize-gp-datasets.smk b/workflow/rules/summarize-gp-datasets.smk
@@ -1,12 +1,12 @@
 rule summarize_gp_dataset:
     input:
-        "results/{config_name}/datasets/{config_name}-{event_type}-dataset.fits"
+        "config[path_results]/{config_name}/datasets/{config_name}-{event_type}-dataset.fits"
     output:
-        report("results/{config_name}/summary/images/{event_type}/{config_name}-{event_type}-counts-image.png", caption="../report/caption-counts.rst", category="Counts", subcategory="{event_type}"),
-        report("results/{config_name}/summary/images/{event_type}/{config_name}-{event_type}-counts-grid.png", caption="../report/caption-counts.rst", category="Counts", subcategory="{event_type}"),
+        report("config[path_results]/{config_name}/summary/images/{event_type}/{config_name}-{event_type}-counts-image.png", caption="../report/caption-counts.rst", category="Counts", subcategory="{event_type}"),
+        report("config[path_results]/{config_name}/summary/images/{event_type}/{config_name}-{event_type}-counts-grid.png", caption="../report/caption-counts.rst", category="Counts", subcategory="{event_type}"),
 
-        report("results/{config_name}/summary/images/{event_type}/{config_name}-{event_type}-exposure-image.png", caption="../report/caption-exposure.rst", category="Exposure", subcategory="{event_type}"),
-        report("results/{config_name}/summary/images/{event_type}/{config_name}-{event_type}-exposure-grid.png", caption="../report/caption-exposure.rst", category="Exposure", subcategory="{event_type}"),
+        report("config[path_results]/{config_name}/summary/images/{event_type}/{config_name}-{event_type}-exposure-image.png", caption="../report/caption-exposure.rst", category="Exposure", subcategory="{event_type}"),
+        report("config[path_results]/{config_name}/summary/images/{event_type}/{config_name}-{event_type}-exposure-grid.png", caption="../report/caption-exposure.rst", category="Exposure", subcategory="{event_type}"),
     log:
         "logs/{config_name}/{event_type}/prepare-gp-dataset.log"
     run:

diff --git a/workflow/rules/summarize-gp-spectra.smk b/workflow/rules/summarize-gp-spectra.smk
@@ -1,10 +1,10 @@
 rule summarize_gp_spectra:
     input:
-        "results/{config_name}/datasets/{config_name}-datasets-all.yaml"
+        "config[path_results]/{config_name}/datasets/{config_name}-datasets-all.yaml"
     output:
-        report("results/{config_name}/summary/images/{config_name}-counts-spectra.png", caption="../report/caption-counts.rst", category="Counts"),
-        report("results/{config_name}/summary/images/{config_name}-exposure-spectra.png", caption="../report/caption-counts.rst", category="Exposure"),
-        report("results/{config_name}/summary/images/{config_name}-psf-spectra.png", caption="../report/caption-counts.rst", category="PSF"),
+        report("config[path_results]/{config_name}/summary/images/{config_name}-counts-spectra.png", caption="../report/caption-counts.rst", category="Counts"),
+        report("config[path_results]/{config_name}/summary/images/{config_name}-exposure-spectra.png", caption="../report/caption-counts.rst", category="Exposure"),
+        report("config[path_results]/{config_name}/summary/images/{config_name}-psf-spectra.png", caption="../report/caption-counts.rst", category="PSF"),
     log:
         "logs/{config_name}/summarize-gp-spectra.log"
     run: