Merge pull request #88 from bcbi/dpa/refactor-api

Refactor the API to make it more reusable

Author: DilumAluthge

.github/workflows/ci.yml

@@ -15,6 +15,7 @@ jobs:
     strategy:
       matrix:
         version:
+          - '1.4'
           - '1'
           - 'nightly'
         os:
@@ -31,3 +32,7 @@ jobs:
       - uses: julia-actions/julia-runtest@latest
         env:
           SIMPLECONTAINERGENERATOR_TESTS: 'all'
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/predictmd.yml

@@ -1,4 +1,4 @@
-name: PredictMD
+name: PredictMD_docker
 on:
   pull_request:
   push:
@@ -10,7 +10,7 @@ on:
     - cron: '00 00,12 * * *'
 
 jobs:
-  PredictMD:
+  PredictMD_docker:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -28,7 +28,7 @@ jobs:
           arch: ${{ matrix.arch }}
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest
-      - run: julia --project -e 'import SimpleContainerGenerator; pkgs = [(name = "PredictMD", rev = "master", ), (name = "PredictMDExtra", rev = "master", ), (name = "PredictMDFull", rev = "master", ), (name = "UnicodePlots", version = "1.2.0 - *", ),]; no_test = String["UnicodePlots"]; parent_image = "nvidia/cuda"; SimpleContainerGenerator.create_dockerfile(pkgs; no_test = no_test, parent_image = parent_image)'
+      - run: julia --project -e 'import SimpleContainerGenerator; pkgs = [(name = "PredictMD", rev = "master", ), (name = "PredictMDExtra", rev = "master", ), (name = "PredictMDFull", rev = "master", ), (name = "UnicodePlots", version = "1.2.0 - *", ),]; no_test = String["UnicodePlots"]; parent_image = "nvidia/cuda"; tests_must_pass = String["PredictMD", "PredictMDExtra", "PredictMDFull"]; SimpleContainerGenerator.create_dockerfile(pkgs; no_test = no_test, parent_image = parent_image, tests_must_pass = tests_must_pass)'
       - if: github.ref == 'refs/heads/master' && (github.event_name == 'push' || github.event_name == 'schedule')
         env:
           DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}

.travis.yml

@@ -1,7 +1,7 @@
 name = "SimpleContainerGenerator"
 uuid = "b8d349fb-717b-4aac-a9b1-e1da4219c631"
 authors = ["Dilum Aluthge"]
-version = "1.3.0"
+version = "2.0.0-DEV"
 
 [deps]
 PackageCompiler = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d"

Project.toml

@@ -1,7 +1,7 @@
 # SimpleContainerGenerator
 
-[![Build Status](https://travis-ci.com/bcbi/SimpleContainerGenerator.jl.svg?branch=master)](https://travis-ci.com/bcbi/SimpleContainerGenerator.jl/branches)
-[![Codecov](https://codecov.io/gh/bcbi/SimpleContainerGenerator.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/bcbi/SimpleContainerGenerator.jl)
+[![Build Status](https://github.com/bcbi/SimpleContainerGenerator.jl/workflows/CI/badge.svg)](https://github.com/bcbi/SimpleContainerGenerator.jl/actions)
+[![Coverage](https://codecov.io/gh/bcbi/SimpleContainerGenerator.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/bcbi/SimpleContainerGenerator.jl)
 
 SimpleContainerGenerator automates the process of creating container images for using Julia packages.
 
@@ -20,6 +20,8 @@ Pkg.add("SimpleContainerGenerator")
 
 ## Examples
 
+In order to run these examples, you will need to have Docker installed on your computer.
+
 ### Example 1
 
 ```julia
@@ -35,9 +37,9 @@ pkgs = [
 ]
 julia_version = v"1.4.0"
 
-SimpleContainerGenerator.create_dockerfile(pkgs,
-                                           pwd();
-                                           julia_version = julia_version)
+SimpleContainerGenerator.create_dockerfile(pkgs;
+                                           julia_version = julia_version,
+                                           output_directory = pwd())
 
 run(`docker build -t my_docker_username/my_image_name .`)
 ```
@@ -57,9 +59,9 @@ pkgs = [
 ]
 julia_version = v"1.4.0"
 
-SimpleContainerGenerator.create_dockerfile(pkgs,
-                                           pwd();
-                                           julia_version = julia_version)
+SimpleContainerGenerator.create_dockerfile(pkgs;
+                                           julia_version = julia_version,
+                                           output_directory = pwd())
 
 run(`docker build -t my_docker_username/my_image_name .`)
 ```
@@ -79,9 +81,9 @@ pkgs = [
 ]
 julia_version = v"1.4.0"
 
-SimpleContainerGenerator.create_dockerfile(pkgs,
-                                           pwd();
-                                           julia_version = julia_version)
+SimpleContainerGenerator.create_dockerfile(pkgs;
+                                           julia_version = julia_version,
+                                           output_directory = pwd())
 
 run(`docker build -t my_docker_username/my_image_name .`)
 ```
@@ -101,9 +103,9 @@ pkgs = [
 ]
 julia_version = v"1.4.0"
 
-SimpleContainerGenerator.create_dockerfile(pkgs,
-                                           pwd();
-                                           julia_version = julia_version)
+SimpleContainerGenerator.create_dockerfile(pkgs;
+                                           julia_version = julia_version,
+                                           output_directory = pwd())
 
 run(`docker build -t my_docker_username/my_image_name .`)
 ```
@@ -129,11 +131,11 @@ exclude_packages_from_sysimage = [
     ]
 julia_version = v"1.4.0"
 
-SimpleContainerGenerator.create_dockerfile(pkgs,
-                                           pwd();
+SimpleContainerGenerator.create_dockerfile(pkgs;
                                            julia_version = julia_version,
                                            no_test = no_test,
-                                           exclude_packages_from_sysimage = exclude_packages_from_sysimage)
+                                           exclude_packages_from_sysimage = exclude_packages_from_sysimage,
+                                           output_directory = pwd())
 
 run(`docker build -t my_docker_username/my_image_name .`)
 ```
@@ -154,9 +156,9 @@ pkgs = [
 julia_version = v"1.4.0"
 parent_image = "ubuntu:latest"
 
-SimpleContainerGenerator.create_dockerfile(pkgs,
-                                           pwd();
+SimpleContainerGenerator.create_dockerfile(pkgs;
                                            julia_version = julia_version,
+                                           output_directory = pwd(),
                                            parent_image = parent_image)
 
 run(`docker build -t my_docker_username/my_image_name .`)
@@ -178,9 +180,9 @@ pkgs = [
 julia_version = v"1.4.0"
 parent_image = "nvidia/cuda:latest"
 
-SimpleContainerGenerator.create_dockerfile(pkgs,
-                                           pwd();
+SimpleContainerGenerator.create_dockerfile(pkgs;
                                            julia_version = julia_version,
+                                           output_directory = pwd(),
                                            parent_image = parent_image)
 
 run(`docker build -t my_docker_username/my_image_name .`)
@@ -203,4 +205,4 @@ run(`docker build -t my_docker_username/my_image_name .`)
 
 ## Acknowledgements
 
-- This work was supported in part by National Institutes of Health grants U54GM115677, R01LM011963, and R25MH116440. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
+- This work was supported in part by National Institutes of Health grants R01LM011963, R25MH116440, and U54GM115677 and National Science Foundation award 2027892. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the National Science Foundation.

README.md

@@ -4,14 +4,15 @@ import PackageCompiler
 import Pkg
 import UUIDs
 
+include("types_config.jl")
 include("types.jl")
 
 include("public.jl")
-
 include("public_create_dockerfile.jl")
 
 include("assert.jl")
 include("backups_of_simplecontainergenerator.jl")
+include("config_to_template.jl")
 include("default_values.jl")
 include("docker.jl")
 include("generate_helper_files.jl")
@@ -20,6 +21,7 @@ include("generate_packagecompiler_install.jl")
 include("generate_packagecompiler_run.jl")
 include("generate_precompile_execution.jl")
 include("julia.jl")
+include("pkg_dir.jl")
 include("utils.jl")
 
 end # module

src/SimpleContainerGenerator.jl

@@ -1,4 +1,4 @@
-@inline function always_assert(condition::Bool,
+function always_assert(condition::Bool,
                                msg::String)
     if !condition
         throw(AlwaysAssertionError(msg))

src/assert.jl

@@ -1,4 +1,4 @@
-@inline function _generate_backupsofsimplecontainergenerator_content_1(config::Config)
+function _generate_backupsofsimplecontainergenerator_content_1(config::Config)
     simplecontainergenerator_installation_command = config.simplecontainergenerator_installation_command
     lines = String[
         "empty!(Base.DEPOT_PATH)",
@@ -10,7 +10,7 @@
     return content
 end
 
-@inline function _generate_backupsofsimplecontainergenerator_content_2(config::Config)
+function _generate_backupsofsimplecontainergenerator_content_2(config::Config)
     packagecompiler_installation_command = config.packagecompiler_installation_command
     lines = String[
         "empty!(Base.DEPOT_PATH)",