Combined plot optimization

SMHviz_plot/utils_data.py

@@ -206,7 +206,9 @@ def sample_df(df, scenario, pathogen, k=1000):
         all_sample_sel = list(np.random.permutation(all_sample_sel))
         df_sample_sel = df_scen.reset_index().set_index("sample_id").loc[all_sample_sel]
         all_sample = df_sample_sel.reset_index().drop(columns="index")
-        all_sample["sample_id_n"] = list(np.repeat(list(range(k)), len(df_scen['horizon'].drop_duplicates())))
+
+        all_sample["sample_id_n"] = np.repeat(np.arange(k), len(df_scen['horizon'].drop_duplicates()))
+
         all_sample = all_sample[["value", "target_end_date", "sample_id_n"]]
         all_sample = all_sample.rename(columns={"value": "value" + "_" + pathogen})
     else:
@@ -223,7 +225,7 @@ def q1(x):
     :type x: pd.Series
     :return: float
     """
-    return x.quantile(0.025)
+    return np.quantile(x, 0.025)
 
 
 def q2(x):
@@ -235,7 +237,7 @@ def q2(x):
     :type x: pd.Series
     :return: float
     """
-    return x.quantile(0.05)
+    return np.quantile(x, 0.05)
 
 
 def q3(x):
@@ -247,7 +249,7 @@ def q3(x):
     :type x: pd.Series
     :return: float
     """
-    return x.quantile(0.1)
+    return np.quantile(x, 0.1)
 
 
 def q4(x):
@@ -259,7 +261,7 @@ def q4(x):
     :type x: pd.Series
     :return: float
     """
-    return x.quantile(0.25)
+    return np.quantile(x, 0.25)
 
 
 def q5(x):
@@ -271,7 +273,7 @@ def q5(x):
     :type x: pd.Series
     :return: float
     """
-    return x.quantile(0.75)
+    return np.quantile(x, 0.75)
 
 
 def q6(x):
@@ -283,7 +285,7 @@ def q6(x):
     :type x: pd.Series
     :return: float
     """
-    return x.quantile(0.9)
+    return np.quantile(x, 0.9)
 
 
 def q7(x):
@@ -295,7 +297,7 @@ def q7(x):
     :type x: pd.Series
     :return: float
     """
-    return x.quantile(0.95)
+    return np.quantile(x, 0.95)
 
 
 def q8(x):
@@ -307,7 +309,7 @@ def q8(x):
     :type x: pd.Series
     :return: float
     """
-    return x.quantile(0.975)
+    return np.quantile(x, 0.975)
 
 
 def med(x):
@@ -319,7 +321,7 @@ def med(x):
     :type x: pd.Series
     :return: float
     """
-    return x.quantile(0.5)
+    return np.quantile(x, 0.5)
 
 
 def mean(x):
@@ -391,9 +393,9 @@ def prep_multipat_plot_comb(pathogen_information, calc_mean=False):
         # Preparation
         pathogen_name = patho.lower()
         if calc_mean is True:
-            f2.update({"proportion_" + pathogen_name: [med, mean, q1, q2, q3, q4, q5, q6, q7, q8]})
+            f2.update({"proportion_" + pathogen_name: [mean, q4, q5]})
         else:
-            f2.update({"proportion_" + pathogen_name: [med, q1, q2, q3, q4, q5, q6, q7, q8]})
+            f2.update({"proportion_" + pathogen_name: [q4, q5]})
         all_sample["proportion_" + pathogen_name] = all_sample["value_" + pathogen_name] / all_sample["value"]
     # Calculate the quantiles for each "value" and "proportion" columns
     all_quantile = all_sample.groupby(["target_end_date"]).agg(f)

changelog.md

@@ -0,0 +1,7 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## 0.0.1 
+
+First version

docs/release_protocol.md

@@ -0,0 +1,153 @@
+# Release Process
+
+Parts of this document is adapted for the U.S. Scenario Modeling Hub (SMH) from 
+[The Hubverse](https://hubverse-org.github.io/hubDevs/articles/release-process.html) 
+and from 
+[The Carpentries Developer's Handbook](https://carpentries.github.io/workbench-dev/releases.html) ©
+The Carpentries under the 
+[CC-BY 4.0 license](https://creativecommons.org/licenses/by/4.0/). 
+
+## Workflow
+
+The release process follow a general workflow:
+
+1. Iterate on small bug fixes and PRs on branches:
+   - merging into `main` once ready to publish/deploy
+   - merging into a development branch (here called `dev`) for ongoing test/process
+2. When ready to release on `main`: bump the version, add an annotated git tag, and release
+3. Bump the version in main back to a development version
+
+Some of the steps in these instructions are specific for R packages, but they are largely process-based 
+and can apply to Python packages as well.
+
+### Versioning 
+
+The SMH is built using very basic semantic versioning using the X.Y.Z[.9000] pattern. Everything that 
+has a .9000 attached is considered in-development.
+
+`X`: **Major version number**:  this version number will change if there are significant breaking 
+changes to any of the user-facing workflows. That is, if a change requires users to modify their 
+scripts, then it is a breaking change.
+
+`Y`: **Minor version number**: this version number will change if there are new features or
+ enhanced behaviors available to the users in a way that *does not affect how users who do not 
+need the new features use the package*. This number grows the fastest in early stages of development.
+
+`Z`: **Patch version number**: this version number will change if something that was previously 
+broken was fixed, but no new features have been added.
+
+`9000`: **Development version indicator**: this version number indicates that the package is in a 
+development state and has the potential to change. When its on the main branch, it indicates 
+that the features or patches introduced have been reviewed and tested. This version is appended 
+after every successful release. 
+
+###  Hotfixes
+
+A hotfix is a bug fix for a situation where a bug has been found, but the main branch has new features 
+that are not yet ready to be released.
+
+## Checklist
+
+### Updates
+
+[] Create new branch from `main` (or `master`, or branch of interest) called `"<author initial>/<feature>/<issue>"`
+
+[] Update `Changelog.md` accordingly
+
+[] Commit, push
+
+[] Open Pull-Request (PR) on branch of interest (`main` for release we want to implement quickly or ready to deploy, other 
+ branch of interest for ongoing updates)
+
+[] Merge after review, once all accepted 
+
+**Create new release version only if important change, see version**
+
+### Release
+
+[] Create new branch from `main` (or `master`) called `"<author>/release/X.Y.Z"`
+
+[] Update `pyproject.toml` and `Changelog.md` accordingly
+
+[] Commit, push
+
+[] Open Pull-Request (PR)
+
+[] Merge after review, once all accepted 
+
+[] Checkout `main` branch (or `master`) & make sure it's up to date
+
+[] Add new tag
+
+```
+git tag -a v.X.Y.Z -m '<short message>'
+git push --tags
+```
+
+[] Create a new release on GitHub (can be done using R, for example)
+
+```r
+usethis::use_github_release()
+```
+
+### Post-Release
+
+[] Create new branch from `main` (or `master`) called `"post-release-X.Y.Z"`
+
+[] Set project to dev version (can be done using R, for example): 
+	- adding `.9000` to the version number
+	-  adding new heading to `Changelog.md` (`## <package name> (development)`)
+
+```r
+usethis::use_dev_version()
+```
+
+[] Commit, push, open Pull-Request (PR) 
+
+[] Merge after review, once all accepted 
+
+
+### Subsequent updates
+
+[] Create new branch from `main` (or `master`, or branch of interest) called `"<author initial>/<feature>/<issue>"`
+
+[] Update `Changelog.md` accordingly
+
+[] Commit, push
+
+[] Open Pull-Request (PR)
+
+[] Merge after review, once all accepted 
+
+**Create new release version only if important change, see version**
+
+### Hotfixes
+
+[] Create new branch from `main` (or `master`) called `"<author>/hotfix/<issue>"`
+
+```	
+git switch --detach v.X.Y.Z'
+git switch -c <author>/hotfix/<issue>
+```
+
+[] Write a test, fix the bug, commit, push
+** Don't change the version **
+
+[] Open Pull-Request (PR) 
+
+[] Update `Changelog.md` accordingly and bump the patch version in `pyproject.toml`
+
+```
+git commit -m 'bump version to X.Y.Z+1'
+git tag -a v.X.Y.Z+1 -m '<short message>'
+git push
+git push --tags
+```
+
+[] Create a new release on GitHub (can be done using R, for example)
+
+```r
+usethis::use_github_release()
+```
+
+[] Resolve conflicts in PR & merge into `main` (or `master`)