New package structure, explicit importing from modules is required

tomasstolker · Nov 6, 2023 · 081263d · 081263d
1 parent 27f4ee4
commit 081263d
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diff --git a/Makefile b/Makefile
@@ -20,6 +20,7 @@ docs:
 	rm -f docs/species.analysis.rst
 	rm -f docs/species.core.rst
 	rm -f docs/species.data.rst
+	rm -f docs/species.phot.rst
 	rm -f docs/species.plot.rst
 	rm -f docs/species.read.rst
 	rm -f docs/species.util.rst

diff --git a/docs/species.analysis.rst b/docs/species.analysis.rst
@@ -4,6 +4,14 @@ species.analysis package
 Submodules
 ----------
 
+species.analysis.atmo\_retrieval module
+---------------------------------------
+
+.. automodule:: species.analysis.atmo_retrieval
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 species.analysis.compare\_spectra module
 ----------------------------------------
 
@@ -44,22 +52,6 @@ species.analysis.fit\_spectrum module
    :undoc-members:
    :show-inheritance:
 
-species.analysis.photometry module
-----------------------------------
-
-.. automodule:: species.analysis.photometry
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-species.analysis.retrieval module
----------------------------------
-
-.. automodule:: species.analysis.retrieval
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 Module contents
 ---------------
 

diff --git a/docs/species.core.rst b/docs/species.core.rst
@@ -20,10 +20,10 @@ species.core.constants module
    :undoc-members:
    :show-inheritance:
 
-species.core.init module
-------------------------
+species.core.species\_init module
+---------------------------------
 
-.. automodule:: species.core.init
+.. automodule:: species.core.species_init
    :members:
    :undoc-members:
    :show-inheritance:

diff --git a/docs/species.phot.rst b/docs/species.phot.rst
@@ -0,0 +1,21 @@
+species.phot package
+====================
+
+Submodules
+----------
+
+species.phot.syn\_phot module
+-----------------------------
+
+.. automodule:: species.phot.syn_phot
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: species.phot
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/species.rst b/docs/species.rst
@@ -9,6 +9,7 @@ Subpackages
     species.analysis
     species.core
     species.data
+    species.phot
     species.plot
     species.read
     species.util

diff --git a/docs/species.util.rst b/docs/species.util.rst
@@ -4,6 +4,14 @@ species.util package
 Submodules
 ----------
 
+species.util.convert\_util module
+---------------------------------
+
+.. automodule:: species.util.convert_util
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 species.util.data\_util module
 ------------------------------
 
@@ -20,6 +28,14 @@ species.util.dust\_util module
    :undoc-members:
    :show-inheritance:
 
+species.util.model\_util module
+-------------------------------
+
+.. automodule:: species.util.model_util
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 species.util.phot\_util module
 ------------------------------
 
@@ -44,6 +60,14 @@ species.util.query\_util module
    :undoc-members:
    :show-inheritance:
 
+species.util.radtrans\_util module
+----------------------------------
+
+.. automodule:: species.util.radtrans_util
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 species.util.read\_util module
 ------------------------------
 
@@ -60,6 +84,14 @@ species.util.retrieval\_util module
    :undoc-members:
    :show-inheritance:
 
+species.util.spec\_util module
+------------------------------
+
+.. automodule:: species.util.spec_util
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 species.util.test\_util module
 ------------------------------