Merge pull request #69 from PharmCat/Remove-NCA

clean
PharmCat · Jan 17, 2025 · 303af8e · 303af8e · PharmCat · Jan 17, 2025
2 parents e9daefd + fcdc272
commit 303af8e
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diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
diff --git a/.github/workflows/Documenter.yml b/.github/workflows/Documenter.yml
@@ -19,14 +19,13 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    timeout-minutes: 30
+    timeout-minutes: 45
     steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
-          version: "1"
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-docdeploy@v1
+          version: "1.8"
+      - uses: julia-actions/cache@v1
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

diff --git a/.github/workflows/Tier1.yml b/.github/workflows/Tier1.yml
@@ -30,26 +30,36 @@ jobs:
     strategy:
       matrix:
         version:
-          - '1.6'
-          - '1.7'
           - '1.8'
+          - '1'
         os:
           - ubuntu-latest
           - macOS-latest
           - windows-latest
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: julia-actions/cache@v1
+      - uses: actions/cache@v4
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
+        if: ${{ matrix.os == 'ubuntu-latest' && matrix.version == '1' && matrix.arch == 'x64' }}
         with:
-          files: lcov.info
+          file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
 
diff --git a/Project.toml b/Project.toml
@@ -16,7 +16,7 @@ Distributions = "0.21, 0.22, 0.23, 0.24, 0.25"
 QuadGK = "1, 2"
 Roots = "1, 2"
 SpecialFunctions = "1, 2"
-StatsBase = "0.30, 0.31, 0.32, 0.33"
+StatsBase = "0.30, 0.31, 0.32, 0.33, 0.34"
 julia = "1"
 
 [extras]

diff --git a/change.log b/change.log
@@ -1,6 +1,9 @@
+V0.7.1
+  - Clean.
+
 V0.7.0
   - Stay only sample size, power and randomization. Other functions moved to another packages.
-  - Change licance.
+  - Change licence.
 
 v0.6.2
   - Minor fix

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,12 +1,9 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 
 [compat]
 
-Documenter = "0.23, 0.24, 0.25, 0.26"
+Documenter = "≥0.26"
 DataFrames = "0.22, 1"
-CSV = "0.6, 0.7, 0.8"
-Plots = "1"
+
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,4 +1,4 @@
-using Documenter, ClinicalTrialUtilities, DataFrames, CSV, Plots
+using Documenter, ClinicalTrialUtilities, DataFrames
 
 makedocs(
     modules = [ClinicalTrialUtilities],
@@ -17,4 +17,4 @@ makedocs(
     ],
 )
 
-deploydocs(repo = "github.com/PharmCat/ClinicalTrialUtilities.jl.git")
+deploydocs(repo = "github.com/PharmCat/ClinicalTrialUtilities.jl.git", push_preview = true)
diff --git a/docs/src/ci.md b/docs/src/ci.md
diff --git a/docs/src/ds.md b/docs/src/ds.md
diff --git a/docs/src/export.md b/docs/src/export.md
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -10,13 +10,14 @@
 
 ## Description
 
-The package is designed to perform calculations related to the planning of clinical trials.
+The package is designed to perform sample size calculations for clinical trials.
+
 ## Installation
 ```
 using Pkg; Pkg.add("ClinicalTrialUtilities");
 ```
 
-### Pharmacodynamics
+### Note
 
 Further development of NCA PK/PD will be based on [MetidaNCA.jl](https://github.com/PharmCat/MetidaNCA.jl) package.
 
@@ -39,10 +40,6 @@ When ctpower/ctsamplen used:
 - :ei - Equivalencens: two one-sided hypothesis;
 - :ns - Non-Inferiority / Superiority: one-sided hypothesis, for some cases you should use two-sided hypothesis for  Non-Inferiority/Superiority, you can use alpha/2 for this;
 
-## Invalidated version v0.3.0 (removed from release page)
-
-  Wrong Equivalence Hypothesis alpha level! Use 0.2.7, 0.3.1 version or higher.
-
 ## Contents
 
 ```@contents

diff --git a/docs/src/nca.md b/docs/src/nca.md
diff --git a/docs/src/pd.md b/docs/src/pd.md
diff --git a/docs/src/samplesize.md b/docs/src/samplesize.md
@@ -55,3 +55,9 @@ ClinicalTrialUtilities.ctsamplen
 ```@docs
 ClinicalTrialUtilities.besamplen
 ```
+## See also 
+
+### ctask 
+```@docs
+ClinicalTrialUtilities.ctask 
+```
diff --git a/docs/src/sim.md b/docs/src/sim.md
diff --git a/docs/src/utils.md b/docs/src/utils.md
@@ -5,11 +5,26 @@
 ClinicalTrialUtilities.cvfromci
 ```
 
+### cvfromsd
+```@docs
+ClinicalTrialUtilities.cvfromsd
+```
+
 ### cvfromvar
 ```@docs
 ClinicalTrialUtilities.cvfromvar
 ```
 
+### sdfromcv
+```@docs
+ClinicalTrialUtilities.sdfromcv
+```
+
+### varfromcv 
+```@docs
+ClinicalTrialUtilities.varfromcv 
+```
+
 ### pooledcv
 ```@docs
 ClinicalTrialUtilities.pooledcv

diff --git a/docs/src/validation.md b/docs/src/validation.md
diff --git a/docs/validation/Descriptive Stats Julia Test.spv b/docs/validation/Descriptive Stats Julia Test.spv
diff --git a/docs/validation/Descriptive Stats Julia Test.xls b/docs/validation/Descriptive Stats Julia Test.xls
diff --git a/docs/validation/Julia test.phxproj b/docs/validation/Julia test.phxproj
diff --git a/docs/validation/PD.csv b/docs/validation/PD.csv