Added cumulative incidence to `summary_longformat.xlsx`

CHANGES:

1.  Added code in `summary_longformat.py` to calculate cumulative incidence;
2.  Switched from `openpyxl` to `xlsxwriter` for lower memory usage when writing
    to summary_longformat.xlsx.

covid/tasks/summary_longformat.py

@@ -116,6 +116,13 @@ def summary_longformat(input_files, output_file):
     medium_df["value_name"] = "absolute_incidence"
     df = pd.concat([df, medium_df], axis="index")
 
+    # Cumulative cases
+    medium_df = xarray2summarydf(
+        medium_term["events"][..., 2].cumsum(dim="time").reset_coords(drop=True)
+    )
+    medium_df["value_name"] = "cumulative_absolute_incidence"
+    df = pd.concat([df, medium_df], axis="index")
+
     # Medium term incidence per 100k
     medium_df = xarray2summarydf(
         (

pyproject.toml

@@ -18,7 +18,6 @@ descartes = "^1.1.0"
 matplotlib = "^3.3.2"
 xlrd = "^1.2.0"
 tqdm = "^4.50.2"
-openpyxl = "^3.0.5"
 h5py = "^2.10.0"
 gemlib = {git = "http://fhm-chicas-code.lancs.ac.uk/GEM/gemlib.git"}
 xarray = "^0.16.1"
@@ -26,6 +25,7 @@ seaborn = "^0.11.0"
 ruffus = "^2.8.4"
 tensorflow = "^2.4.0"
 jedi = "^0.17.2"
+XlsxWriter = "^1.3.7"
 
 [tool.poetry.dev-dependencies]
 ipython = "^7.18.1"