From e0efda83168fe7cb6d2a3ae13cf268f663a8b7e2 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 12:45:48 +0000
Subject: [PATCH 01/37] Rename `CI` to `Tests`

---
 .github/workflows/Tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index 17b8c0e89..a5a89ab0d 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -1,4 +1,4 @@
-name: CI
+name: Tests
 
 on:
   push:

From 621410913d9ed3ae846b9d3cf9b219a50131d475 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 13:12:25 +0000
Subject: [PATCH 02/37] a bit of formatting

---
 .github/workflows/Tests.yml | 25 ++++++++++---------------
 1 file changed, 10 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index a5a89ab0d..8d216a783 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -2,28 +2,23 @@ name: Tests
 
 on:
   push:
-    branches:
-      - master
+    branches: ["master"]
   pull_request:
 
+  workflow_dispatch:
+
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    name: Julia ${{ matrix.version }} on ${{ matrix.os }} (${{ matrix.arch }})
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ matrix.version == 'nightly' }}
     strategy:
       fail-fast: false
       matrix:
-        version:
-          - '1'
-          - '1.9'
-          - 'nightly'
-        os:
-          - ubuntu-latest
-          - macOS-latest
-          - windows-latest
-        arch:
-          - x64
+        version: ['1', '1.9', 'nightly']
+        os: [ubuntu-latest, macOS-latest, windows-latest]
+        arch: [x64]
+        # specific config for codecov
         include:
           - version: '1'
             os: ubuntu-latest
@@ -36,8 +31,6 @@ jobs:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
       - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
         with:
           path: ~/.julia/artifacts
           key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
@@ -45,6 +38,8 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
+        env:
+          cache-name: cache-artifacts
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1

From 1d412b2a19484e2580ea0510f07f08f08751be11 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 13:13:34 +0000
Subject: [PATCH 03/37] update `checkout` and `cache` actions to v4

---
 .github/workflows/Tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index 8d216a783..9e51482aa 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -25,12 +25,12 @@ jobs:
             arch: x64
             coverage: true
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+      - uses: actions/cache@v4
         with:
           path: ~/.julia/artifacts
           key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}

From 202d5c6af7b56f5d381eee73e1b2214bee65acd7 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 13:24:27 +0000
Subject: [PATCH 04/37] cache packages

---
 .github/workflows/Tests.yml | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index 9e51482aa..091b3f833 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -24,27 +24,30 @@ jobs:
             os: ubuntu-latest
             arch: x64
             coverage: true
+    env:
+      CACHE_NAME: julia-${{ matrix.version }}-${{ matrix.arch }}
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v4
+      - name: Cache Julia packages and artifacts
+        uses: actions/cache@v4
         with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          path: |
+            ~/.julia
+            ~/.julia/artifacts
+          key: ${{ runner.os }}-${{ env.CACHE_NAME }}-${{ hashFiles('**/Project.toml', '**/Manifest.toml') }}
           restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
-        env:
-          cache-name: cache-artifacts
+            ${{ runner.os }}-${{ env.CACHE_NAME }}-
+            ${{ runner.os }}-julia-${{ matrix.version }}-
+            ${{ runner.os }}-julia-
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.coverage
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v4
         if: matrix.coverage
         with:
           file: lcov.info

From 08227e8b1fcbe2bdeb6cc2f3626f163d4e7dfa27 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 14:00:30 +0000
Subject: [PATCH 05/37] add CompatHelper

---
 .github/workflows/CompatHelper.yml | 45 ++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 .github/workflows/CompatHelper.yml

diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
new file mode 100644
index 000000000..3dfba52e8
--- /dev/null
+++ b/.github/workflows/CompatHelper.yml
@@ -0,0 +1,45 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
\ No newline at end of file

From f8a07456ed1597d930c821bc4b7ae918a1a31b91 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 14:05:54 +0000
Subject: [PATCH 06/37] move `methadone` to `BUGSExample`, not enabled

---
 {test => src/BUGSExamples/Volume_4}/methadone/README.md    | 0
 {test => src/BUGSExamples/Volume_4}/methadone/data1.csv    | 0
 {test => src/BUGSExamples/Volume_4}/methadone/data2.csv    | 0
 {test => src/BUGSExamples/Volume_4}/methadone/methadone.jl | 0
 4 files changed, 0 insertions(+), 0 deletions(-)
 rename {test => src/BUGSExamples/Volume_4}/methadone/README.md (100%)
 rename {test => src/BUGSExamples/Volume_4}/methadone/data1.csv (100%)
 rename {test => src/BUGSExamples/Volume_4}/methadone/data2.csv (100%)
 rename {test => src/BUGSExamples/Volume_4}/methadone/methadone.jl (100%)

diff --git a/test/methadone/README.md b/src/BUGSExamples/Volume_4/methadone/README.md
similarity index 100%
rename from test/methadone/README.md
rename to src/BUGSExamples/Volume_4/methadone/README.md
diff --git a/test/methadone/data1.csv b/src/BUGSExamples/Volume_4/methadone/data1.csv
similarity index 100%
rename from test/methadone/data1.csv
rename to src/BUGSExamples/Volume_4/methadone/data1.csv
diff --git a/test/methadone/data2.csv b/src/BUGSExamples/Volume_4/methadone/data2.csv
similarity index 100%
rename from test/methadone/data2.csv
rename to src/BUGSExamples/Volume_4/methadone/data2.csv
diff --git a/test/methadone/methadone.jl b/src/BUGSExamples/Volume_4/methadone/methadone.jl
similarity index 100%
rename from test/methadone/methadone.jl
rename to src/BUGSExamples/Volume_4/methadone/methadone.jl

From 96cf29d3543b6a5f5eadb86117b2d0ba8099dcb9 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 14:06:28 +0000
Subject: [PATCH 07/37] remove `gradient_tests`

---
 test/gradient_tests/blockers.csv | 48 -----------------------
 test/gradient_tests/rats.csv     | 66 --------------------------------
 2 files changed, 114 deletions(-)
 delete mode 100755 test/gradient_tests/blockers.csv
 delete mode 100755 test/gradient_tests/rats.csv

diff --git a/test/gradient_tests/blockers.csv b/test/gradient_tests/blockers.csv
deleted file mode 100755
index 4350df1a8..000000000
--- a/test/gradient_tests/blockers.csv
+++ /dev/null
@@ -1,48 +0,0 @@
-param,label,value,diffs AD,diffs FD
-mu[1],0,0.0,-32.5,-32.5
-mu[2],1,0.0,-94.0,-94.0
-mu[3],2,0.0,-65.0,-65.0
-mu[4],3,0.0,-1297.5,-1297.5
-mu[5],4,0.0,-305.0,-305.0
-mu[6],5,0.0,-45.5,-45.50000001
-mu[7],6,0.0,-692.0,-692.0
-mu[8],7,0.0,-443.5,-443.5
-mu[9],8,0.0,-218.0,-218.0
-mu[10],9,0.0,-1592.5,-1592.5
-mu[11],10,0.0,-612.0,-612.0
-mu[12],11,0.0,-172.5,-172.5
-mu[13],12,0.0,-267.0,-267.0
-mu[14],13,0.0,-768.5,-768.5
-mu[15],14,0.0,-94.5,-94.5
-mu[16],15,0.0,-139.0,-139.0
-mu[17],16,0.0,-146.5,-146.5
-mu[18],17,0.0,-138.5,-138.5
-mu[19],18,0.0,-145.0,-145.0
-mu[20],19,0.0,-141.5,-141.5
-mu[21],20,0.0,-307.5,-307.5
-mu[22],21,0.0,-616.0,-616.0
-delta[1],22,0.0,-16.0,-16.0
-delta[2],23,0.0,-50.0,-49.99999999
-delta[3],24,0.0,-29.5,-29.5
-delta[4],25,0.0,-664.5,-664.5
-delta[5],26,0.0,-149.5,-149.5
-delta[6],27,0.0,-25.5,-25.5
-delta[7],28,0.0,-374.5,-374.5
-delta[8],29,0.0,-256.0,-256.0
-delta[9],30,0.0,-114.0,-114.0
-delta[10],31,0.0,-820.0,-820.0
-delta[11],32,0.0,-372.5,-372.5
-delta[12],33,0.0,-86.5,-86.5
-delta[13],34,0.0,-136.5,-136.5
-delta[14],35,0.0,-372.0,-372.0
-delta[15],36,0.0,-52.0,-52.00000001
-delta[16],37,0.0,-70.5,-70.5
-delta[17],38,0.0,-97.5,-97.5
-delta[18],39,0.0,-67.5,-67.5
-delta[19],40,0.0,-81.0,-81.0
-delta[20],41,0.0,-72.5,-72.5
-delta[21],42,0.0,-168.5,-168.5
-delta[22],43,0.0,-318.0,-318.0
-d,44,1.0,0.0,0.0
-tau,45,0.0,11.5,11.5
-delta.new,46,0.0,0.0,0.0
diff --git a/test/gradient_tests/rats.csv b/test/gradient_tests/rats.csv
deleted file mode 100755
index 1a8b53a3f..000000000
--- a/test/gradient_tests/rats.csv
+++ /dev/null
@@ -1,66 +0,0 @@
-param,label,value,diffs AD,diffs FD
-alpha[1],0,250.0,-151.0,-151.0
-alpha[2],1,250.0,-110.0,-110.0
-alpha[3],2,250.0,-86.0,-86.00000001
-alpha[4],3,250.0,-189.0,-189.0
-alpha[5],4,250.0,-194.0,-194.0
-alpha[6],5,250.0,-100.0,-100.0000001
-alpha[7],6,250.0,-209.0,-209.0
-alpha[8],7,250.0,-107.0,-107.0
-alpha[9],8,250.0,74.0,74.00000002
-alpha[10],9,250.0,-258.0,-257.9999999
-alpha[11],10,250.0,-56.0,-55.99999989
-alpha[12],11,250.0,-212.0,-212.0
-alpha[13],12,250.0,-138.0,-138.0
-alpha[14],13,250.0,-4.0,-4.000000044
-alpha[15],14,250.0,-136.0,-135.9999999
-alpha[16],15,250.0,-123.0,-122.9999999
-alpha[17],16,250.0,-191.0,-190.9999999
-alpha[18],17,250.0,-148.0,-147.9999999
-alpha[19],18,250.0,-79.0,-78.99999997
-alpha[20],19,250.0,-142.0,-141.9999999
-alpha[21],20,250.0,-106.0,-105.9999999
-alpha[22],21,250.0,-227.0,-227.0
-alpha[23],22,250.0,-210.0,-210.0000001
-alpha[24],23,250.0,-124.0,-124.0000001
-alpha[25],24,250.0,-179.0,-179.0000001
-alpha[26],25,250.0,-78.0,-78.00000007
-alpha[27],26,250.0,-76.0,-76.00000012
-alpha[28],27,250.0,-135.0,-135.0
-alpha[29],28,250.0,-265.0,-265.0000001
-alpha[30],29,250.0,-143.0,-143.0000001
-beta[1],30,6.0,18.0,17.99999998
-beta[2],31,6.0,648.0,647.9999999
-beta[3],32,6.0,284.0,283.9999998
-beta[4],33,6.0,-444.0,-444.0000001
-beta[5],34,6.0,340.0,339.9999999
-beta[6],35,6.0,88.0,87.99999981
-beta[7],36,6.0,-38.0,-38.00000006
-beta[8],37,6.0,242.0,241.9999999
-beta[9],38,6.0,648.0,647.9999999
-beta[10],39,6.0,-122.0,-122.0000001
-beta[11],40,6.0,487.0,486.9999998
-beta[12],41,6.0,53.0,52.9999999
-beta[13],42,6.0,81.0,80.99999992
-beta[14],43,6.0,417.0,416.9999999
-beta[15],44,6.0,-395.0,-395.0000001
-beta[16],45,6.0,-73.0,-73.00000012
-beta[17],46,6.0,151.0,150.9999999
-beta[18],47,6.0,-122.0,-122.0000001
-beta[19],48,6.0,235.0,234.9999998
-beta[20],49,6.0,11.0,10.99999994
-beta[21],50,6.0,235.0,234.9999998
-beta[22],51,6.0,-115.0,-115.0000002
-beta[23],52,6.0,-185.0,-185.0000001
-beta[24],53,6.0,-94.0,-94.0000001
-beta[25],54,6.0,557.0,557.0
-beta[26],55,6.0,326.0,325.9999998
-beta[27],56,6.0,-87.0,-87.00000006
-beta[28],57,6.0,-122.0,-122.0
-beta[29],58,6.0,-234.0,-234.0000001
-beta[30],59,6.0,60.0,59.99999994
-tau.c,60,1.0,-23485.0,-23485.00004
-alpha.c,61,150.0,2999.99985,2999.99985
-alpha.tau,62,1.0,-149985.0,-149985.0002
-beta.c,63,10.0,-120.00001,-120.0000069
-beta.tau,64,1.0,-225.0,-224.9999975

From f63318e8129ecabc355d200376642c1350f2a7f3 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 14:24:39 +0000
Subject: [PATCH 08/37] rename BUGSExample folder name

---
 src/BUGSExamples/BUGSExamples.jl              | 50 +++++++++----------
 .../{Volume_I => Volume_1}/Blocker.jl         |  0
 .../{Volume_I => Volume_1}/Bones.jl           |  0
 .../{Volume_I => Volume_1}/Dogs.jl            |  0
 .../{Volume_I => Volume_1}/Dyes.jl            |  0
 .../{Volume_I => Volume_1}/Epil.jl            |  0
 .../{Volume_I => Volume_1}/Equiv.jl           |  0
 .../{Volume_I => Volume_1}/Inhalers.jl        |  0
 .../{Volume_I => Volume_1}/Kidney.jl          |  0
 .../{Volume_I => Volume_1}/LSAT.jl            |  0
 .../{Volume_I => Volume_1}/Leuk.jl            |  0
 .../{Volume_I => Volume_1}/LeukFr.jl          |  0
 .../{Volume_I => Volume_1}/Magnesium.jl       |  0
 .../{Volume_I => Volume_1}/Mice.jl            |  0
 .../{Volume_I => Volume_1}/Oxford.jl          |  0
 .../{Volume_I => Volume_1}/Pumps.jl           |  0
 .../{Volume_I => Volume_1}/Rats.jl            |  0
 .../{Volume_I => Volume_1}/Salm.jl            |  0
 .../{Volume_I => Volume_1}/Seeds.jl           |  0
 .../{Volume_I => Volume_1}/Stacks.jl          |  0
 .../{Volume_I => Volume_1}/Surgical.jl        |  0
 .../{Volume_II => Volume_2}/Alligators.jl     |  0
 .../{Volume_II => Volume_2}/BiRats.jl         |  0
 .../{Volume_II => Volume_2}/Eyes.jl           |  0
 src/compiler_pass.jl                          |  2 +-
 src/utils.jl                                  |  8 +--
 test/runtests.jl                              | 19 +------
 27 files changed, 32 insertions(+), 47 deletions(-)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Blocker.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Bones.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Dogs.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Dyes.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Epil.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Equiv.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Inhalers.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Kidney.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/LSAT.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Leuk.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/LeukFr.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Magnesium.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Mice.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Oxford.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Pumps.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Rats.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Salm.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Seeds.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Stacks.jl (100%)
 rename src/BUGSExamples/{Volume_I => Volume_1}/Surgical.jl (100%)
 rename src/BUGSExamples/{Volume_II => Volume_2}/Alligators.jl (100%)
 rename src/BUGSExamples/{Volume_II => Volume_2}/BiRats.jl (100%)
 rename src/BUGSExamples/{Volume_II => Volume_2}/Eyes.jl (100%)

diff --git a/src/BUGSExamples/BUGSExamples.jl b/src/BUGSExamples/BUGSExamples.jl
index 5582374b1..6609ada77 100644
--- a/src/BUGSExamples/BUGSExamples.jl
+++ b/src/BUGSExamples/BUGSExamples.jl
@@ -2,31 +2,31 @@ module BUGSExamples
 
 using JuliaBUGS: @bugs
 
-include("Volume_I/Blocker.jl")
-include("Volume_I/Bones.jl")
-include("Volume_I/Dogs.jl")
-include("Volume_I/Dyes.jl")
-include("Volume_I/Epil.jl")
-include("Volume_I/Equiv.jl")
-include("Volume_I/Inhalers.jl")
-include("Volume_I/Kidney.jl")
-include("Volume_I/Leuk.jl")
-include("Volume_I/LeukFr.jl")
-include("Volume_I/LSAT.jl")
-include("Volume_I/Magnesium.jl")
-include("Volume_I/Mice.jl")
-include("Volume_I/Oxford.jl")
-include("Volume_I/Pumps.jl")
-include("Volume_I/Rats.jl")
-include("Volume_I/Salm.jl")
-include("Volume_I/Seeds.jl")
-include("Volume_I/Stacks.jl")
-include("Volume_I/Surgical.jl")
+include("Volume_1/Blocker.jl")
+include("Volume_1/Bones.jl")
+include("Volume_1/Dogs.jl")
+include("Volume_1/Dyes.jl")
+include("Volume_1/Epil.jl")
+include("Volume_1/Equiv.jl")
+include("Volume_1/Inhalers.jl")
+include("Volume_1/Kidney.jl")
+include("Volume_1/Leuk.jl")
+include("Volume_1/LeukFr.jl")
+include("Volume_1/LSAT.jl")
+include("Volume_1/Magnesium.jl")
+include("Volume_1/Mice.jl")
+include("Volume_1/Oxford.jl")
+include("Volume_1/Pumps.jl")
+include("Volume_1/Rats.jl")
+include("Volume_1/Salm.jl")
+include("Volume_1/Seeds.jl")
+include("Volume_1/Stacks.jl")
+include("Volume_1/Surgical.jl")
 
-include("Volume_II/BiRats.jl")
-include("Volume_II/Eyes.jl")
+include("Volume_2/BiRats.jl")
+include("Volume_2/Eyes.jl")
 
-const VOLUME_I = (
+const VOLUME_1 = (
     blockers=blockers,
     bones=bones,
     dogs=dogs,
@@ -50,10 +50,10 @@ const VOLUME_I = (
     surgical_realistic=surgical_realistic,
 )
 
-const VOLUME_II = (birats=birats, eyes=eyes)
+const VOLUME_2 = (birats=birats, eyes=eyes)
 
 function has_ground_truth(m::Symbol)
-    if m in union(keys(VOLUME_I), keys(VOLUME_II))
+    if m in union(keys(VOLUME_1), keys(VOLUME_2))
         return haskey(getfield(BUGSExamples, m), :reference_results)
     else
         return false
diff --git a/src/BUGSExamples/Volume_I/Blocker.jl b/src/BUGSExamples/Volume_1/Blocker.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Blocker.jl
rename to src/BUGSExamples/Volume_1/Blocker.jl
diff --git a/src/BUGSExamples/Volume_I/Bones.jl b/src/BUGSExamples/Volume_1/Bones.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Bones.jl
rename to src/BUGSExamples/Volume_1/Bones.jl
diff --git a/src/BUGSExamples/Volume_I/Dogs.jl b/src/BUGSExamples/Volume_1/Dogs.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Dogs.jl
rename to src/BUGSExamples/Volume_1/Dogs.jl
diff --git a/src/BUGSExamples/Volume_I/Dyes.jl b/src/BUGSExamples/Volume_1/Dyes.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Dyes.jl
rename to src/BUGSExamples/Volume_1/Dyes.jl
diff --git a/src/BUGSExamples/Volume_I/Epil.jl b/src/BUGSExamples/Volume_1/Epil.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Epil.jl
rename to src/BUGSExamples/Volume_1/Epil.jl
diff --git a/src/BUGSExamples/Volume_I/Equiv.jl b/src/BUGSExamples/Volume_1/Equiv.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Equiv.jl
rename to src/BUGSExamples/Volume_1/Equiv.jl
diff --git a/src/BUGSExamples/Volume_I/Inhalers.jl b/src/BUGSExamples/Volume_1/Inhalers.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Inhalers.jl
rename to src/BUGSExamples/Volume_1/Inhalers.jl
diff --git a/src/BUGSExamples/Volume_I/Kidney.jl b/src/BUGSExamples/Volume_1/Kidney.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Kidney.jl
rename to src/BUGSExamples/Volume_1/Kidney.jl
diff --git a/src/BUGSExamples/Volume_I/LSAT.jl b/src/BUGSExamples/Volume_1/LSAT.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/LSAT.jl
rename to src/BUGSExamples/Volume_1/LSAT.jl
diff --git a/src/BUGSExamples/Volume_I/Leuk.jl b/src/BUGSExamples/Volume_1/Leuk.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Leuk.jl
rename to src/BUGSExamples/Volume_1/Leuk.jl
diff --git a/src/BUGSExamples/Volume_I/LeukFr.jl b/src/BUGSExamples/Volume_1/LeukFr.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/LeukFr.jl
rename to src/BUGSExamples/Volume_1/LeukFr.jl
diff --git a/src/BUGSExamples/Volume_I/Magnesium.jl b/src/BUGSExamples/Volume_1/Magnesium.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Magnesium.jl
rename to src/BUGSExamples/Volume_1/Magnesium.jl
diff --git a/src/BUGSExamples/Volume_I/Mice.jl b/src/BUGSExamples/Volume_1/Mice.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Mice.jl
rename to src/BUGSExamples/Volume_1/Mice.jl
diff --git a/src/BUGSExamples/Volume_I/Oxford.jl b/src/BUGSExamples/Volume_1/Oxford.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Oxford.jl
rename to src/BUGSExamples/Volume_1/Oxford.jl
diff --git a/src/BUGSExamples/Volume_I/Pumps.jl b/src/BUGSExamples/Volume_1/Pumps.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Pumps.jl
rename to src/BUGSExamples/Volume_1/Pumps.jl
diff --git a/src/BUGSExamples/Volume_I/Rats.jl b/src/BUGSExamples/Volume_1/Rats.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Rats.jl
rename to src/BUGSExamples/Volume_1/Rats.jl
diff --git a/src/BUGSExamples/Volume_I/Salm.jl b/src/BUGSExamples/Volume_1/Salm.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Salm.jl
rename to src/BUGSExamples/Volume_1/Salm.jl
diff --git a/src/BUGSExamples/Volume_I/Seeds.jl b/src/BUGSExamples/Volume_1/Seeds.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Seeds.jl
rename to src/BUGSExamples/Volume_1/Seeds.jl
diff --git a/src/BUGSExamples/Volume_I/Stacks.jl b/src/BUGSExamples/Volume_1/Stacks.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Stacks.jl
rename to src/BUGSExamples/Volume_1/Stacks.jl
diff --git a/src/BUGSExamples/Volume_I/Surgical.jl b/src/BUGSExamples/Volume_1/Surgical.jl
similarity index 100%
rename from src/BUGSExamples/Volume_I/Surgical.jl
rename to src/BUGSExamples/Volume_1/Surgical.jl
diff --git a/src/BUGSExamples/Volume_II/Alligators.jl b/src/BUGSExamples/Volume_2/Alligators.jl
similarity index 100%
rename from src/BUGSExamples/Volume_II/Alligators.jl
rename to src/BUGSExamples/Volume_2/Alligators.jl
diff --git a/src/BUGSExamples/Volume_II/BiRats.jl b/src/BUGSExamples/Volume_2/BiRats.jl
similarity index 100%
rename from src/BUGSExamples/Volume_II/BiRats.jl
rename to src/BUGSExamples/Volume_2/BiRats.jl
diff --git a/src/BUGSExamples/Volume_II/Eyes.jl b/src/BUGSExamples/Volume_2/Eyes.jl
similarity index 100%
rename from src/BUGSExamples/Volume_II/Eyes.jl
rename to src/BUGSExamples/Volume_2/Eyes.jl
diff --git a/src/compiler_pass.jl b/src/compiler_pass.jl
index bfffdd453..6a2d3cc4d 100644
--- a/src/compiler_pass.jl
+++ b/src/compiler_pass.jl
@@ -486,7 +486,7 @@ The function returns three values:
 Array elements and array variables are represented by tuples in the returned value. All `Colon` indexing is assumed to be concretized.
 
 # Examples
-```jldoctest
+```jldoctest; setup = :(using JuliaBUGS: evaluate_and_track_dependencies)
 julia> evaluate_and_track_dependencies(:(x[a]), (x=[missing, missing], a = missing))
 (missing, (:a, (:x, 1:2)))
 
diff --git a/src/utils.jl b/src/utils.jl
index da0d43b69..0bc2b1b48 100644
--- a/src/utils.jl
+++ b/src/utils.jl
@@ -88,7 +88,7 @@ end
 Extract all the array variable names and number of dimensions from a given simple expression. 
 
 # Examples:
-```jldoctest
+```jldoctest; setup = :(using JuliaBUGS: extract_variable_names_and_numdims)
 julia> extract_variable_names_and_numdims(:((a + b) * c), ())
 (a = 0, b = 0, c = 0)
 
@@ -154,7 +154,7 @@ will raise an error.
 
 # Example:
 ```jldoctest
-extract_variable_names_and_numdims(
+JuliaBUGS.extract_variable_names_and_numdims(
     @bugs begin
         for i in 1:N
             for j in 1:T
@@ -434,7 +434,7 @@ Replace all `Colon()`s in `expr` with the corresponding array size.
 
 # Examples
 ```jldoctest
-julia> concretize_colon_indexing(:(f(x[1, :])), (x = [1 2 3 4; 5 6 7 8; 9 10 11 12],))
+julia> JuliaBUGS.concretize_colon_indexing(:(f(x[1, :])), (x = [1 2 3 4; 5 6 7 8; 9 10 11 12],))
 :(f(x[1, 1:4]))
 ```
 """
@@ -460,7 +460,7 @@ This function evaluates expressions that consist solely of arithmetic operations
 is specifically designed for scenarios such as calculating array indices or determining loop boundaries.
 
 # Example:
-```jldoctest
+```jldoctest; setup = :(using JuliaBUGS: simple_arithmetic_eval)
 julia> simple_arithmetic_eval((a = 1, b = [1, 2]), 1)
 1
 
diff --git a/test/runtests.jl b/test/runtests.jl
index d9b2680dd..45308ed01 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -5,8 +5,7 @@ using AdvancedMH
 using Bijectors
 using Distributions
 using Documenter
-using DynamicPPL
-using DynamicPPL: getlogp, settrans!!, SimpleVarInfo
+using DynamicPPL: DynamicPPL, getlogp, settrans!!, SimpleVarInfo
 using Graphs, MetaGraphsNext
 using JuliaBUGS
 using JuliaBUGS:
@@ -37,21 +36,7 @@ if get(ENV, "RUN_MODE", "test") == "profile"
     include("profile.jl")
 else
     @testset "Function Unit Tests" begin
-        DocMeta.setdocmeta!(
-            JuliaBUGS,
-            :DocTestSetup,
-            :(using JuliaBUGS:
-                JuliaBUGS,
-                BUGSExamples,
-                @bugs,
-                evaluate_and_track_dependencies,
-                evaluate,
-                concretize_colon_indexing,
-                extract_variable_names_and_numdims,
-                extract_variables_in_bounds_and_lhs_indices,
-                simple_arithmetic_eval);
-            recursive=true,
-        )
+        DocMeta.setdocmeta!(JuliaBUGS, :DocTestSetup, :(using JuliaBUGS); recursive=true)
         Documenter.doctest(JuliaBUGS; manual=false)
     end
 

From 78c19514806ef6a3f348420610486dae86887098 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 14:43:37 +0000
Subject: [PATCH 09/37] factorize tests into different CI tasks

---
 .github/workflows/Benchmark.yml               | 59 -------------
 .github/workflows/Tests.yml                   | 12 +++
 src/BUGSExamples/BUGSExamples.jl              |  2 +-
 test/logp_tests/{ => BUGS_models}/blockers.jl |  0
 test/logp_tests/{ => BUGS_models}/bones.jl    |  0
 test/logp_tests/{ => BUGS_models}/dogs.jl     |  0
 test/logp_tests/{ => BUGS_models}/rats.jl     |  0
 .../binomial.jl                               |  0
 .../ddirich.jl                                |  0
 .../dwish.jl                                  |  0
 .../gamma.jl                                  |  0
 .../{ => single_distribution _models}/lkj.jl  |  0
 test/logp_tests/test_logp.jl                  | 12 +++
 test/runtests.jl                              | 85 ++++++-------------
 14 files changed, 51 insertions(+), 119 deletions(-)
 delete mode 100644 .github/workflows/Benchmark.yml
 rename test/logp_tests/{ => BUGS_models}/blockers.jl (100%)
 rename test/logp_tests/{ => BUGS_models}/bones.jl (100%)
 rename test/logp_tests/{ => BUGS_models}/dogs.jl (100%)
 rename test/logp_tests/{ => BUGS_models}/rats.jl (100%)
 rename test/logp_tests/{ => single_distribution _models}/binomial.jl (100%)
 rename test/logp_tests/{ => single_distribution _models}/ddirich.jl (100%)
 rename test/logp_tests/{ => single_distribution _models}/dwish.jl (100%)
 rename test/logp_tests/{ => single_distribution _models}/gamma.jl (100%)
 rename test/logp_tests/{ => single_distribution _models}/lkj.jl (100%)
 create mode 100644 test/logp_tests/test_logp.jl

diff --git a/.github/workflows/Benchmark.yml b/.github/workflows/Benchmark.yml
deleted file mode 100644
index 4ac8f6f9f..000000000
--- a/.github/workflows/Benchmark.yml
+++ /dev/null
@@ -1,59 +0,0 @@
-name: Benchmarking
-
-on:
-    push:
-        branches:
-            - main
-        tags: ['*']
-    pull_request:
-
-jobs:
-  profile:
-    name: Benchmarking Analysis Passes
-    runs-on: ubuntu-latest
-    continue-on-error: ${{ matrix.version == 'nightly' }}
-    strategy:
-      fail-fast: false
-      matrix:
-        version:
-          - '1'
-        os:
-          - ubuntu-latest
-        arch:
-          - x64
-        include:
-          - version: '1'
-            os: ubuntu-latest
-            arch: x64
-            coverage: false
-    steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        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
-        env:
-            RUN_MODE: profile
-      - uses: julia-actions/julia-processcoverage@v1
-        if: matrix.coverage
-      - uses: codecov/codecov-action@v1
-        if: matrix.coverage
-        with:
-          file: lcov.info
-      - uses: coverallsapp/github-action@master
-        if: matrix.coverage
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          path-to-lcov: lcov.info
diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index 091b3f833..c2b67bc8b 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -18,6 +18,16 @@ jobs:
         version: ['1', '1.9', 'nightly']
         os: [ubuntu-latest, macOS-latest, windows-latest]
         arch: [x64]
+        test_group:
+          - 'profile'
+          - 'unit'
+          - 'parser'
+          - 'analysis_passes'
+          - 'compile_BUGS_examples'
+          - 'corner_cases'
+          - 'graph'
+          - 'gibbs'
+          - 'mcmchains'
         # specific config for codecov
         include:
           - version: '1'
@@ -45,6 +55,8 @@ jobs:
             ${{ runner.os }}-julia-
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+        env:
+          TEST_GROUP: ${{ matrix.test_group }}
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.coverage
       - uses: codecov/codecov-action@v4
diff --git a/src/BUGSExamples/BUGSExamples.jl b/src/BUGSExamples/BUGSExamples.jl
index 6609ada77..599aa2ac1 100644
--- a/src/BUGSExamples/BUGSExamples.jl
+++ b/src/BUGSExamples/BUGSExamples.jl
@@ -33,7 +33,7 @@ const VOLUME_1 = (
     dyes=dyes,
     epil=epil,
     equiv=equiv,
-    inhalers=inhalers,
+    # inhalers=inhalers,
     kidney=kidney,
     leuk=leuk,
     leukfr=leukfr,
diff --git a/test/logp_tests/blockers.jl b/test/logp_tests/BUGS_models/blockers.jl
similarity index 100%
rename from test/logp_tests/blockers.jl
rename to test/logp_tests/BUGS_models/blockers.jl
diff --git a/test/logp_tests/bones.jl b/test/logp_tests/BUGS_models/bones.jl
similarity index 100%
rename from test/logp_tests/bones.jl
rename to test/logp_tests/BUGS_models/bones.jl
diff --git a/test/logp_tests/dogs.jl b/test/logp_tests/BUGS_models/dogs.jl
similarity index 100%
rename from test/logp_tests/dogs.jl
rename to test/logp_tests/BUGS_models/dogs.jl
diff --git a/test/logp_tests/rats.jl b/test/logp_tests/BUGS_models/rats.jl
similarity index 100%
rename from test/logp_tests/rats.jl
rename to test/logp_tests/BUGS_models/rats.jl
diff --git a/test/logp_tests/binomial.jl b/test/logp_tests/single_distribution _models/binomial.jl
similarity index 100%
rename from test/logp_tests/binomial.jl
rename to test/logp_tests/single_distribution _models/binomial.jl
diff --git a/test/logp_tests/ddirich.jl b/test/logp_tests/single_distribution _models/ddirich.jl
similarity index 100%
rename from test/logp_tests/ddirich.jl
rename to test/logp_tests/single_distribution _models/ddirich.jl
diff --git a/test/logp_tests/dwish.jl b/test/logp_tests/single_distribution _models/dwish.jl
similarity index 100%
rename from test/logp_tests/dwish.jl
rename to test/logp_tests/single_distribution _models/dwish.jl
diff --git a/test/logp_tests/gamma.jl b/test/logp_tests/single_distribution _models/gamma.jl
similarity index 100%
rename from test/logp_tests/gamma.jl
rename to test/logp_tests/single_distribution _models/gamma.jl
diff --git a/test/logp_tests/lkj.jl b/test/logp_tests/single_distribution _models/lkj.jl
similarity index 100%
rename from test/logp_tests/lkj.jl
rename to test/logp_tests/single_distribution _models/lkj.jl
diff --git a/test/logp_tests/test_logp.jl b/test/logp_tests/test_logp.jl
new file mode 100644
index 000000000..0c691c54b
--- /dev/null
+++ b/test/logp_tests/test_logp.jl
@@ -0,0 +1,12 @@
+@testset "Log joint probability" begin
+    @testset "Single distribution models" begin
+        @testset "$s" for s in [:binomial, :gamma, :lkj, :dwish, :ddirich]
+            include("./single_distribution_models/$s.jl")
+        end
+    end
+    @testset "BUGS models" begin
+        @testset "$s" for s in [:blockers, :bones, :dogs, :rats]
+            include("./BUGS_models/$s.jl")
+        end
+    end
+end
diff --git a/test/runtests.jl b/test/runtests.jl
index 45308ed01..077d07fcc 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -32,78 +32,45 @@ using Test
 
 AbstractMCMC.setprogress!(false)
 
-if get(ENV, "RUN_MODE", "test") == "profile"
+const test_group = get(ENV, "TEST_GROUP", "")
+
+if test_group == "profile"
     include("profile.jl")
-else
-    @testset "Function Unit Tests" begin
+elseif test_group == "unit"
+    @testset "doctests" begin
         DocMeta.setdocmeta!(JuliaBUGS, :DocTestSetup, :(using JuliaBUGS); recursive=true)
         Documenter.doctest(JuliaBUGS; manual=false)
     end
-
-    include("bugs_primitives.jl")
-
+    include("utils.jl")
+elseif test_group == "parser"
     @testset "Parser" begin
         include("parser/bugs_macro.jl")
         include("parser/bugs_parser.jl")
         include("parser/winbugs_examples.jl")
     end
-
-    include("compile.jl")
-
-    include("cumulative_density.jl")
-
-    @testset "Compile WinBUGS Vol I examples: $m" for m in [
-        :blockers,
-        :bones,
-        :dogs,
-        :dyes,
-        :epil,
-        :equiv,
-        :kidney,
-        :leuk,
-        :leukfr,
-        :lsat,
-        :magnesium,
-        :mice,
-        :oxford,
-        :pumps,
-        :rats,
-        :salm,
-        :seeds,
-        :stacks,
-        :surgical_simple,
-        :surgical_realistic,
-    ]
-        model_def = JuliaBUGS.BUGSExamples.VOLUME_I[m].model_def
-        data = JuliaBUGS.BUGSExamples.VOLUME_I[m].data
-        inits = JuliaBUGS.BUGSExamples.VOLUME_I[m].inits[1]
-        model = compile(model_def, data, inits)
-    end
-
-    @testset "Utils" begin
-        include("utils.jl")
-    end
-
+elseif test_group == "analysis_passes"
     include("passes.jl")
-
-    @testset "Log Probability Test" begin
-        @testset "Single stochastic variable test" begin
-            @testset "test for $s" for s in [:binomial, :gamma, :lkj, :dwish, :ddirich]
-                include("logp_tests/$s.jl")
-            end
-        end
-        @testset "BUGS examples" begin
-            @testset "test for $s" for s in [:blockers, :bones, :dogs, :rats]
-                include("logp_tests/$s.jl")
-            end
+elseif test_group == "compile_BUGS_examples"
+    @testset "BUGS examples volume 1" begin
+        @testset "$m"  for m in keys(JuliaBUGS.BUGSExamples.VOLUME_I)
+            model_def = JuliaBUGS.BUGSExamples.VOLUME_I[m].model_def
+            data = JuliaBUGS.BUGSExamples.VOLUME_I[m].data
+            inits = JuliaBUGS.BUGSExamples.VOLUME_I[m].inits[1]
+            model = compile(model_def, data, inits)
         end
     end
-
-    @testset "Graph data structure" begin
-        include("graphs.jl")
+elseif test_group == "corner_cases"
+    @testset "Some corner cases" begin
+        include("bugs_primitives.jl")
+        include("compile.jl")
+        include("cumulative_density.jl")     
     end
-
+elseif test_group == "graph"
+    include("graphs.jl")
+elseif test_group == "gibbs"
     include("gibbs.jl")
-
+elseif test_group == "mcmchains"
     include("ext/mcmchains.jl")
+else
+    # nothing
 end

From 71e5113e9da9a15ef7ba45d784f9eecb8ea890c2 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 14:44:48 +0000
Subject: [PATCH 10/37] add Test_group to CI name

---
 .github/workflows/Tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index c2b67bc8b..ad8fb75bf 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -9,7 +9,7 @@ on:
 
 jobs:
   test:
-    name: Julia ${{ matrix.version }} on ${{ matrix.os }} (${{ matrix.arch }})
+    name: Julia ${{ matrix.version }} on ${{ matrix.os }} (${{ matrix.arch }}) ${{ matrix.test_group }}
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ matrix.version == 'nightly' }}
     strategy:

From cb1d0ba785668fe4f8f5ccfe74d1048ed694fad0 Mon Sep 17 00:00:00 2001
From: Xianda Sun <5433119+sunxd3@users.noreply.github.com>
Date: Sun, 24 Mar 2024 14:45:48 +0000
Subject: [PATCH 11/37] Update test/runtests.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 test/runtests.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/runtests.jl b/test/runtests.jl
index 077d07fcc..01e776a69 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -52,7 +52,7 @@ elseif test_group == "analysis_passes"
     include("passes.jl")
 elseif test_group == "compile_BUGS_examples"
     @testset "BUGS examples volume 1" begin
-        @testset "$m"  for m in keys(JuliaBUGS.BUGSExamples.VOLUME_I)
+        @testset "$m" for m in keys(JuliaBUGS.BUGSExamples.VOLUME_I)
             model_def = JuliaBUGS.BUGSExamples.VOLUME_I[m].model_def
             data = JuliaBUGS.BUGSExamples.VOLUME_I[m].data
             inits = JuliaBUGS.BUGSExamples.VOLUME_I[m].inits[1]

From fee107c9b71e941cc6a9ddb3ee7425bb915f87eb Mon Sep 17 00:00:00 2001
From: Xianda Sun <5433119+sunxd3@users.noreply.github.com>
Date: Sun, 24 Mar 2024 14:45:52 +0000
Subject: [PATCH 12/37] Update test/runtests.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 test/runtests.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/runtests.jl b/test/runtests.jl
index 01e776a69..587dc0bf9 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -63,7 +63,7 @@ elseif test_group == "corner_cases"
     @testset "Some corner cases" begin
         include("bugs_primitives.jl")
         include("compile.jl")
-        include("cumulative_density.jl")     
+        include("cumulative_density.jl")
     end
 elseif test_group == "graph"
     include("graphs.jl")

From 49be6cbb518f1434416260be0e25ab3ae1f3c899 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 14:58:26 +0000
Subject: [PATCH 13/37] propagate name changes

---
 docs/src/example.md                  |  2 +-
 test/inference.jl                    | 16 ++++++++--------
 test/logp_tests/BUGS_models/bones.jl |  6 +++---
 test/logp_tests/BUGS_models/dogs.jl  |  6 +++---
 test/profile.jl                      |  6 +++---
 test/runtests.jl                     |  8 ++++----
 test/utils.jl                        |  6 +++---
 7 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/docs/src/example.md b/docs/src/example.md
index 99537de0a..bb9a74a3b 100644
--- a/docs/src/example.md
+++ b/docs/src/example.md
@@ -276,4 +276,4 @@ Note that the `init_params` argument is now a vector of initial parameters for e
 Sometimes the progress logger can cause problems in distributed setting, so we can disable it by setting `progress = false`.
 
 ## More Examples
-We have transcribed all the examples from the first volume of the BUGS Examples ([original](https://www.multibugs.org/examples/latest/VolumeI.html) and [transcribed](https://github.com/TuringLang/JuliaBUGS.jl/tree/master/src/BUGSExamples/Volume_I)). All programs and data are included, and can be compiled using the steps described in the tutorial above.
\ No newline at end of file
+We have transcribed all the examples from the first volume of the BUGS Examples ([original](https://www.multibugs.org/examples/latest/VolumeI.html) and [transcribed](https://github.com/TuringLang/JuliaBUGS.jl/tree/master/src/BUGSExamples/VOLUME_1)). All programs and data are included, and can be compiled using the steps described in the tutorial above.
\ No newline at end of file
diff --git a/test/inference.jl b/test/inference.jl
index 337e7a99c..ed26be864 100644
--- a/test/inference.jl
+++ b/test/inference.jl
@@ -46,9 +46,9 @@ end
     end
 
     @testset "Inference results on examples: $m" for m in [:seeds, :rats, :equiv, :stacks]
-        data = JuliaBUGS.BUGSExamples.VOLUME_I[m].data
-        inits = JuliaBUGS.BUGSExamples.VOLUME_I[m].inits[1]
-        model = JuliaBUGS.compile(JuliaBUGS.BUGSExamples.VOLUME_I[m].model_def, data, inits)
+        data = JuliaBUGS.BUGSExamples.VOLUME_1[m].data
+        inits = JuliaBUGS.BUGSExamples.VOLUME_1[m].inits[1]
+        model = JuliaBUGS.compile(JuliaBUGS.BUGSExamples.VOLUME_1[m].model_def, data, inits)
 
         ad_model = ADgradient(:ReverseDiff, model; compile=Val(true))
 
@@ -68,7 +68,7 @@ end
         )
 
         @assert JuliaBUGS.BUGSExamples.has_ground_truth(m) "No reference inference results for $m"
-        ref_inference_results = JuliaBUGS.BUGSExamples.VOLUME_I[m].reference_results
+        ref_inference_results = JuliaBUGS.BUGSExamples.VOLUME_1[m].reference_results
         @testset "$m: $var" for var in keys(ref_inference_results)
             @test summarize(samples_and_stats)[var].nt.mean[1] ≈
                 ref_inference_results[var].mean rtol = 0.2
@@ -78,10 +78,10 @@ end
     end
 
     @testset "Inference results on examples: m" for m in [:birats]
-        data = JuliaBUGS.BUGSExamples.VOLUME_II[m].data
-        inits = JuliaBUGS.BUGSExamples.VOLUME_II[m].inits[1]
+        data = JuliaBUGS.BUGSExamples.VOLUME_2[m].data
+        inits = JuliaBUGS.BUGSExamples.VOLUME_2[m].inits[1]
         model = JuliaBUGS.compile(
-            JuliaBUGS.BUGSExamples.VOLUME_II[m].model_def, data, inits
+            JuliaBUGS.BUGSExamples.VOLUME_2[m].model_def, data, inits
         )
 
         ad_model = ADgradient(:ReverseDiff, model; compile=Val(true))
@@ -102,7 +102,7 @@ end
         )
 
         @assert JuliaBUGS.BUGSExamples.has_ground_truth(m) "No reference inference results for $m"
-        ref_inference_results = JuliaBUGS.BUGSExamples.VOLUME_II[m].reference_results
+        ref_inference_results = JuliaBUGS.BUGSExamples.VOLUME_2[m].reference_results
         @testset "$m: $var" for var in keys(ref_inference_results)
             @test summarize(samples_and_stats)[var].nt.mean[1] ≈
                 ref_inference_results[var].mean rtol = 0.2
diff --git a/test/logp_tests/BUGS_models/bones.jl b/test/logp_tests/BUGS_models/bones.jl
index 2629979b5..0ef265e4c 100644
--- a/test/logp_tests/BUGS_models/bones.jl
+++ b/test/logp_tests/BUGS_models/bones.jl
@@ -1,6 +1,6 @@
-bugs_model_def = JuliaBUGS.BUGSExamples.VOLUME_I[:bones].model_def
-data = JuliaBUGS.BUGSExamples.VOLUME_I[:bones].data
-inits = JuliaBUGS.BUGSExamples.VOLUME_I[:bones].inits[1]
+bugs_model_def = JuliaBUGS.BUGSExamples.VOLUME_1[:bones].model_def
+data = JuliaBUGS.BUGSExamples.VOLUME_1[:bones].data
+inits = JuliaBUGS.BUGSExamples.VOLUME_1[:bones].inits[1]
 
 bugs_model = compile(bugs_model_def, data, inits)
 vi = bugs_model.varinfo
diff --git a/test/logp_tests/BUGS_models/dogs.jl b/test/logp_tests/BUGS_models/dogs.jl
index 17f8079cc..4cdd83349 100644
--- a/test/logp_tests/BUGS_models/dogs.jl
+++ b/test/logp_tests/BUGS_models/dogs.jl
@@ -1,6 +1,6 @@
-bugs_model_def = JuliaBUGS.BUGSExamples.VOLUME_I[:dogs].model_def
-data = JuliaBUGS.BUGSExamples.VOLUME_I[:dogs].data
-inits = JuliaBUGS.BUGSExamples.VOLUME_I[:dogs].inits[1]
+bugs_model_def = JuliaBUGS.BUGSExamples.VOLUME_1[:dogs].model_def
+data = JuliaBUGS.BUGSExamples.VOLUME_1[:dogs].data
+inits = JuliaBUGS.BUGSExamples.VOLUME_1[:dogs].inits[1]
 
 bugs_model = compile(bugs_model_def, data, inits)
 vi = bugs_model.varinfo
diff --git a/test/profile.jl b/test/profile.jl
index bf99dde3a..0aee38ec8 100644
--- a/test/profile.jl
+++ b/test/profile.jl
@@ -5,10 +5,10 @@ using JuliaBUGS: BUGSExamples
 
 suite = BenchmarkGroup()
 
-for name in keys(BUGSExamples.VOLUME_I)
+for name in keys(BUGSExamples.VOLUME_1)
     @info "Adding benchmark for $name"
-    model_def = BUGSExamples.VOLUME_I[name].model_def
-    data = BUGSExamples.VOLUME_I[name].data
+    model_def = BUGSExamples.VOLUME_1[name].model_def
+    data = BUGSExamples.VOLUME_1[name].data
 
     non_data_scalars, non_data_array_sizes = JuliaBUGS.determine_array_sizes(
         model_def, data
diff --git a/test/runtests.jl b/test/runtests.jl
index 587dc0bf9..b82b08e14 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -52,10 +52,10 @@ elseif test_group == "analysis_passes"
     include("passes.jl")
 elseif test_group == "compile_BUGS_examples"
     @testset "BUGS examples volume 1" begin
-        @testset "$m" for m in keys(JuliaBUGS.BUGSExamples.VOLUME_I)
-            model_def = JuliaBUGS.BUGSExamples.VOLUME_I[m].model_def
-            data = JuliaBUGS.BUGSExamples.VOLUME_I[m].data
-            inits = JuliaBUGS.BUGSExamples.VOLUME_I[m].inits[1]
+        @testset "$m" for m in keys(JuliaBUGS.BUGSExamples.VOLUME_1)
+            model_def = JuliaBUGS.BUGSExamples.VOLUME_1[m].model_def
+            data = JuliaBUGS.BUGSExamples.VOLUME_1[m].data
+            inits = JuliaBUGS.BUGSExamples.VOLUME_1[m].inits[1]
             model = compile(model_def, data, inits)
         end
     end
diff --git a/test/utils.jl b/test/utils.jl
index 13c1b565c..605fb060a 100644
--- a/test/utils.jl
+++ b/test/utils.jl
@@ -22,9 +22,9 @@ end
 # Tests for `getparams`, using `Rats` model
 @testset "`getparams` with Rats" begin
     m = :rats
-    data = JuliaBUGS.BUGSExamples.VOLUME_I[m].data
-    inits = JuliaBUGS.BUGSExamples.VOLUME_I[m].inits[1]
-    model = JuliaBUGS.compile(JuliaBUGS.BUGSExamples.VOLUME_I[m].model_def, data, inits)
+    data = JuliaBUGS.BUGSExamples.VOLUME_1[m].data
+    inits = JuliaBUGS.BUGSExamples.VOLUME_1[m].inits[1]
+    model = JuliaBUGS.compile(JuliaBUGS.BUGSExamples.VOLUME_1[m].model_def, data, inits)
 
     # transformed
     @test LogDensityProblems.logdensity(

From 42248802ac0acadb3d4a3c0f5980334cd4b27502 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 15:02:15 +0000
Subject: [PATCH 14/37] format

---
 test/inference.jl | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/test/inference.jl b/test/inference.jl
index ed26be864..0f2bdec93 100644
--- a/test/inference.jl
+++ b/test/inference.jl
@@ -80,9 +80,7 @@ end
     @testset "Inference results on examples: m" for m in [:birats]
         data = JuliaBUGS.BUGSExamples.VOLUME_2[m].data
         inits = JuliaBUGS.BUGSExamples.VOLUME_2[m].inits[1]
-        model = JuliaBUGS.compile(
-            JuliaBUGS.BUGSExamples.VOLUME_2[m].model_def, data, inits
-        )
+        model = JuliaBUGS.compile(JuliaBUGS.BUGSExamples.VOLUME_2[m].model_def, data, inits)
 
         ad_model = ADgradient(:ReverseDiff, model; compile=Val(true))
 

From 734c085fc9628b2760d37a86a790cbc255065a59 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 15:18:17 +0000
Subject: [PATCH 15/37] use retry for mcmcchains and gibbs

---
 .github/workflows/Tests.yml | 21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index ad8fb75bf..c8cf9b111 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -38,7 +38,8 @@ jobs:
       CACHE_NAME: julia-${{ matrix.version }}-${{ matrix.arch }}
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - name: Set up Julia
+        uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
@@ -52,9 +53,21 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-${{ env.CACHE_NAME }}-
             ${{ runner.os }}-julia-${{ matrix.version }}-
-            ${{ runner.os }}-julia-
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
+            ${{ runner.os }}-julia-${{ matrix.version }}-
+      - name: Build package
+        uses: julia-actions/julia-buildpkg@v1
+      - name: Run tests normally
+        if: matrix.test_group != 'gibbs' && matrix.test_group != 'mcmchains'
+        uses: julia-actions/julia-runtest@v1
+        env:
+          TEST_GROUP: ${{ matrix.test_group }}
+      - name: Run tests with "nick-fields/retry"
+        if: matrix.test_group == 'gibbs' || matrix.test_group == 'mcmchains'
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 10
+          max_attempts : 3
+          command: julia --project -e 'using Pkg; Pkg.instantiate(); Pkg.test(coverage=true)'
         env:
           TEST_GROUP: ${{ matrix.test_group }}
       - uses: julia-actions/julia-processcoverage@v1

From 8eee5dae0273f522a7e7f6325f7af9d775bc3ae0 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 15:29:37 +0000
Subject: [PATCH 16/37] only trigger test run if changes are made to `src` and
 `test`

---
 .github/workflows/Tests.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index c8cf9b111..48b5a912d 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -3,7 +3,13 @@ name: Tests
 on:
   push:
     branches: ["master"]
+    paths:
+      - 'src/**/*'
+      - 'test/**/*'
   pull_request:
+    paths:
+      - 'src/**/*'
+      - 'test/**/*'
 
   workflow_dispatch:
 

From 79e0ea9d6fd62cf4e5e277f6929efec2f0f0fc0a Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 15:32:04 +0000
Subject: [PATCH 17/37] bump version

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index dc30f4c8a..a7c6278c5 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,6 +1,6 @@
 name = "JuliaBUGS"
 uuid = "ba9fb4c0-828e-4473-b6a1-cd2560fee5bf"
-version = "0.5.1"
+version = "0.5.2"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"

From 9b05fb31738b375c5f8b76567a8081da6a08c0e2 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Sun, 24 Mar 2024 15:48:44 +0000
Subject: [PATCH 18/37] add extra clause: run all the tests

---
 test/runtests.jl | 33 ++++++++++++++++++++++++++++++---
 1 file changed, 30 insertions(+), 3 deletions(-)

diff --git a/test/runtests.jl b/test/runtests.jl
index b82b08e14..7cdfa4a9f 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -32,7 +32,7 @@ using Test
 
 AbstractMCMC.setprogress!(false)
 
-const test_group = get(ENV, "TEST_GROUP", "")
+const test_group = get(ENV, "TEST_GROUP", "run_all")
 
 if test_group == "profile"
     include("profile.jl")
@@ -71,6 +71,33 @@ elseif test_group == "gibbs"
     include("gibbs.jl")
 elseif test_group == "mcmchains"
     include("ext/mcmchains.jl")
-else
-    # nothing
+else # run all
+    include("profile.jl")
+    @testset "doctests" begin
+        DocMeta.setdocmeta!(JuliaBUGS, :DocTestSetup, :(using JuliaBUGS); recursive=true)
+        Documenter.doctest(JuliaBUGS; manual=false)
+    end
+    include("utils.jl")
+    @testset "Parser" begin
+        include("parser/bugs_macro.jl")
+        include("parser/bugs_parser.jl")
+        include("parser/winbugs_examples.jl")
+    end
+    include("passes.jl")
+    @testset "BUGS examples volume 1" begin
+        @testset "$m" for m in keys(JuliaBUGS.BUGSExamples.VOLUME_1)
+            model_def = JuliaBUGS.BUGSExamples.VOLUME_1[m].model_def
+            data = JuliaBUGS.BUGSExamples.VOLUME_1[m].data
+            inits = JuliaBUGS.BUGSExamples.VOLUME_1[m].inits[1]
+            model = compile(model_def, data, inits)
+        end
+    end
+    @testset "Some corner cases" begin
+        include("bugs_primitives.jl")
+        include("compile.jl")
+        include("cumulative_density.jl")
+    end
+    include("graphs.jl")
+    include("gibbs.jl")
+    include("ext/mcmchains.jl")
 end

From f57d76735c046d15b7da63d81eb8fbd5daa72047 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 08:08:37 +0000
Subject: [PATCH 19/37] use multiple steps instead of strategy

---
 .github/workflows/Tests.yml | 57 +++++++++++++++++++++++--------------
 1 file changed, 36 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index 48b5a912d..75b66363f 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -15,7 +15,7 @@ on:
 
 jobs:
   test:
-    name: Julia ${{ matrix.version }} on ${{ matrix.os }} (${{ matrix.arch }}) ${{ matrix.test_group }}
+    name: Julia ${{ matrix.version }} on ${{ matrix.os }} (${{ matrix.arch }})
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ matrix.version == 'nightly' }}
     strategy:
@@ -24,17 +24,6 @@ jobs:
         version: ['1', '1.9', 'nightly']
         os: [ubuntu-latest, macOS-latest, windows-latest]
         arch: [x64]
-        test_group:
-          - 'profile'
-          - 'unit'
-          - 'parser'
-          - 'analysis_passes'
-          - 'compile_BUGS_examples'
-          - 'corner_cases'
-          - 'graph'
-          - 'gibbs'
-          - 'mcmchains'
-        # specific config for codecov
         include:
           - version: '1'
             os: ubuntu-latest
@@ -43,7 +32,8 @@ jobs:
     env:
       CACHE_NAME: julia-${{ matrix.version }}-${{ matrix.arch }}
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout
+        uses: actions/checkout@v4
       - name: Set up Julia
         uses: julia-actions/setup-julia@v1
         with:
@@ -59,23 +49,48 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-${{ env.CACHE_NAME }}-
             ${{ runner.os }}-julia-${{ matrix.version }}-
-            ${{ runner.os }}-julia-${{ matrix.version }}-
       - name: Build package
         uses: julia-actions/julia-buildpkg@v1
-      - name: Run tests normally
-        if: matrix.test_group != 'gibbs' && matrix.test_group != 'mcmchains'
+      - name: Running `unit` tests
+        uses: julia-actions/julia-runtest@v1
+        env:
+          TEST_GROUP: unit
+      - name: Running `parser` tests
+        uses: julia-actions/julia-runtest@v1
+        env: 
+          TEST_GROUP: parser
+      - name: Running `analysis_passes` tests
+        uses: julia-actions/julia-runtest@v1
+        env:
+          TEST_GROUP: analysis_passes
+      - name: Running `compile_BUGS_examples` tests
+        uses: julia-actions/julia-runtest@v1
+        env:
+          TEST_GROUP: compile_BUGS_examples
+      - name: Running `corner_cases` tests
         uses: julia-actions/julia-runtest@v1
         env:
-          TEST_GROUP: ${{ matrix.test_group }}
-      - name: Run tests with "nick-fields/retry"
-        if: matrix.test_group == 'gibbs' || matrix.test_group == 'mcmchains'
+          TEST_GROUP: corner_cases
+      - name: Running `graph` tests
+        uses: julia-actions/julia-runtest@v1
+        env:
+          TEST_GROUP: graph
+      - name: Running `gibbs` tests
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 10
+          max_attempts: 3
+          command: julia --project -e 'using Pkg; Pkg.instantiate(); Pkg.test(coverage=true)'
+        env:
+          TEST_GROUP: gibbs
+      - name: Running `mcmchains` tests
         uses: nick-fields/retry@v3
         with:
           timeout_minutes: 10
-          max_attempts : 3
+          max_attempts: 3
           command: julia --project -e 'using Pkg; Pkg.instantiate(); Pkg.test(coverage=true)'
         env:
-          TEST_GROUP: ${{ matrix.test_group }}
+          TEST_GROUP: mcmchains
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.coverage
       - uses: codecov/codecov-action@v4

From 2153de1a7e2e7a0894d954db3d2d25575bcf889f Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 10:28:40 +0000
Subject: [PATCH 20/37] update tests

---
 .github/workflows/Tests.yml  |  48 ++++------------
 test/gibbs.jl                |   7 ++-
 test/graphs.jl               |   3 +
 test/logp_tests/test_logp.jl |   4 ++
 test/parser/test_parser.jl   |   5 ++
 test/runtests.jl             | 108 +++++++++++++++++------------------
 6 files changed, 81 insertions(+), 94 deletions(-)
 create mode 100644 test/parser/test_parser.jl

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index 75b66363f..9e1c33fe5 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -32,15 +32,12 @@ jobs:
     env:
       CACHE_NAME: julia-${{ matrix.version }}-${{ matrix.arch }}
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Set up Julia
-        uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - name: Cache Julia packages and artifacts
-        uses: actions/cache@v4
+      - uses: actions/cache@v4
         with:
           path: |
             ~/.julia
@@ -49,48 +46,23 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-${{ env.CACHE_NAME }}-
             ${{ runner.os }}-julia-${{ matrix.version }}-
-      - name: Build package
-        uses: julia-actions/julia-buildpkg@v1
-      - name: Running `unit` tests
-        uses: julia-actions/julia-runtest@v1
-        env:
-          TEST_GROUP: unit
-      - name: Running `parser` tests
-        uses: julia-actions/julia-runtest@v1
-        env: 
-          TEST_GROUP: parser
-      - name: Running `analysis_passes` tests
-        uses: julia-actions/julia-runtest@v1
-        env:
-          TEST_GROUP: analysis_passes
-      - name: Running `compile_BUGS_examples` tests
-        uses: julia-actions/julia-runtest@v1
-        env:
-          TEST_GROUP: compile_BUGS_examples
-      - name: Running `corner_cases` tests
-        uses: julia-actions/julia-runtest@v1
-        env:
-          TEST_GROUP: corner_cases
-      - name: Running `graph` tests
-        uses: julia-actions/julia-runtest@v1
-        env:
-          TEST_GROUP: graph
+      - uses: julia-actions/julia-buildpkg@v1
+      - name: Running elementary tests
+        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"unit\", \"parser\", \"analysis_passes\", \"graph\"]);"
+      - name: Running compilation tests
+        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"compile_BUGS_examples\", \"corner_cases\", \"logp\"]);"
       - name: Running `gibbs` tests
         uses: nick-fields/retry@v3
         with:
           timeout_minutes: 10
           max_attempts: 3
-          command: julia --project -e 'using Pkg; Pkg.instantiate(); Pkg.test(coverage=true)'
-        env:
-          TEST_GROUP: gibbs
+          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"gibbs\"]);"
       - name: Running `mcmchains` tests
         uses: nick-fields/retry@v3
         with:
           timeout_minutes: 10
           max_attempts: 3
-          command: julia --project -e 'using Pkg; Pkg.instantiate(); Pkg.test(coverage=true)'
-        env:
-          TEST_GROUP: mcmchains
+          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"mcmchains\"]);"
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.coverage
       - uses: codecov/codecov-action@v4
diff --git a/test/gibbs.jl b/test/gibbs.jl
index 973199429..99ad72810 100644
--- a/test/gibbs.jl
+++ b/test/gibbs.jl
@@ -1,3 +1,6 @@
+using JuliaBUGS: MHFromPrior, Gibbs
+using DynamicPPL: DynamicPPL
+
 @testset "Simple gibbs" begin
     model_def = @bugs begin
         # Likelihood
@@ -32,7 +35,9 @@
         :varinfo,
         begin
             vi = model.varinfo
-            SimpleVarInfo(DynamicPPL.values_as(vi, NamedTuple), vi.logp, vi.transformation)
+            DynamicPPL.SimpleVarInfo(
+                DynamicPPL.values_as(vi, NamedTuple), vi.logp, vi.transformation
+            )
         end,
     )
 
diff --git a/test/graphs.jl b/test/graphs.jl
index 6f72f89b5..43af035c0 100644
--- a/test/graphs.jl
+++ b/test/graphs.jl
@@ -1,3 +1,6 @@
+using JuliaBUGS:
+    stochastic_inneighbors, stochastic_neighbors, stochastic_outneighbors, markov_blanket
+
 test_model = @bugs begin
     a ~ dnorm(f, c)
     f = b - 1
diff --git a/test/logp_tests/test_logp.jl b/test/logp_tests/test_logp.jl
index 0c691c54b..a6e511bb5 100644
--- a/test/logp_tests/test_logp.jl
+++ b/test/logp_tests/test_logp.jl
@@ -1,3 +1,7 @@
+using JuliaBUGS:
+    BUGSGraph, DefaultContext, evaluate!!, get_params_varinfo, LogDensityContext
+using DynamicPPL: DynamicPPL, getlogp, settrans!!, SimpleVarInfo
+
 @testset "Log joint probability" begin
     @testset "Single distribution models" begin
         @testset "$s" for s in [:binomial, :gamma, :lkj, :dwish, :ddirich]
diff --git a/test/parser/test_parser.jl b/test/parser/test_parser.jl
new file mode 100644
index 000000000..9d6d0dae7
--- /dev/null
+++ b/test/parser/test_parser.jl
@@ -0,0 +1,5 @@
+@testset "Parser" begin
+    include("bugs_macro.jl")
+    include("bugs_parser.jl")
+    include("winbugs_examples.jl")
+end
diff --git a/test/runtests.jl b/test/runtests.jl
index 7cdfa4a9f..171034716 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -1,95 +1,92 @@
+using JuliaBUGS
+using JuliaBUGS.BUGSPrimitives
+using Documenter
+using Test
+using JuliaBUGS.BUGSPrimitives: mean
+DocMeta.setdocmeta!(JuliaBUGS, :DocTestSetup, :(using JuliaBUGS); recursive=true)
+
 using AbstractPPL
 using AbstractMCMC
 using AdvancedHMC
 using AdvancedMH
 using Bijectors
 using Distributions
-using Documenter
-using DynamicPPL: DynamicPPL, getlogp, settrans!!, SimpleVarInfo
-using Graphs, MetaGraphsNext
-using JuliaBUGS
-using JuliaBUGS:
-    BUGSGraph,
-    DefaultContext,
-    evaluate!!,
-    get_params_varinfo,
-    LogDensityContext,
-    MHFromPrior,
-    stochastic_inneighbors,
-    stochastic_neighbors,
-    stochastic_outneighbors,
-    markov_blanket,
-    Gibbs
-using JuliaBUGS.BUGSPrimitives
-using JuliaBUGS.BUGSPrimitives: mean
+using Graphs
+using MetaGraphsNext
 using LinearAlgebra
-using LogDensityProblems, LogDensityProblemsAD
+using LogDensityProblems
+using LogDensityProblemsAD
 using MacroTools
 using MCMCChains
 using Random
 using ReverseDiff
-using Test
 
 AbstractMCMC.setprogress!(false)
 
-const test_group = get(ENV, "TEST_GROUP", "run_all")
+const Tests = (
+    "profile",
+    "unit",
+    "parser",
+    "analysis_passes",
+    "compile_BUGS_examples",
+    "corner_cases",
+    "graph",
+    "logp",
+    "gibbs",
+    "mcmchains",
+)
+
+for arg in ARGS
+    if arg ∉ Tests
+        error("Unknown test group: $arg")
+    end
+end
 
-if test_group == "profile"
+@info "Running tests for groups: $(ARGS)"
+
+if "profile" in ARGS
     include("profile.jl")
-elseif test_group == "unit"
-    @testset "doctests" begin
-        DocMeta.setdocmeta!(JuliaBUGS, :DocTestSetup, :(using JuliaBUGS); recursive=true)
+elseif "unit" in ARGS
+    @testset "Unit Tests" begin
         Documenter.doctest(JuliaBUGS; manual=false)
+        include("utils.jl")
     end
-    include("utils.jl")
-elseif test_group == "parser"
-    @testset "Parser" begin
-        include("parser/bugs_macro.jl")
-        include("parser/bugs_parser.jl")
-        include("parser/winbugs_examples.jl")
-    end
-elseif test_group == "analysis_passes"
+elseif "parser" in ARGS
+    include("parser/test_parser.jl")
+elseif "analysis_passes" in ARGS
     include("passes.jl")
-elseif test_group == "compile_BUGS_examples"
+elseif "compile_BUGS_examples" in ARGS
     @testset "BUGS examples volume 1" begin
         @testset "$m" for m in keys(JuliaBUGS.BUGSExamples.VOLUME_1)
-            model_def = JuliaBUGS.BUGSExamples.VOLUME_1[m].model_def
-            data = JuliaBUGS.BUGSExamples.VOLUME_1[m].data
-            inits = JuliaBUGS.BUGSExamples.VOLUME_1[m].inits[1]
-            model = compile(model_def, data, inits)
+            m = JuliaBUGS.BUGSExamples.VOLUME_1[m]
+            model = compile(m.model_def, m.data, m.inits[1])
         end
     end
-elseif test_group == "corner_cases"
+elseif "corner_cases" in ARGS
     @testset "Some corner cases" begin
         include("bugs_primitives.jl")
         include("compile.jl")
         include("cumulative_density.jl")
     end
-elseif test_group == "graph"
+elseif "graph" in ARGS
     include("graphs.jl")
-elseif test_group == "gibbs"
+elseif "logp" in ARGS
+    include("logp_tests/test_logp.jl")
+elseif "gibbs" in ARGS
     include("gibbs.jl")
-elseif test_group == "mcmchains"
+elseif "mcmchains" in ARGS
     include("ext/mcmchains.jl")
 else # run all
-    include("profile.jl")
-    @testset "doctests" begin
-        DocMeta.setdocmeta!(JuliaBUGS, :DocTestSetup, :(using JuliaBUGS); recursive=true)
+    @testset "Unit Tests" begin
         Documenter.doctest(JuliaBUGS; manual=false)
+        include("utils.jl")
     end
-    include("utils.jl")
-    @testset "Parser" begin
-        include("parser/bugs_macro.jl")
-        include("parser/bugs_parser.jl")
-        include("parser/winbugs_examples.jl")
-    end
+    include("parser/test_parser.jl")
     include("passes.jl")
     @testset "BUGS examples volume 1" begin
         @testset "$m" for m in keys(JuliaBUGS.BUGSExamples.VOLUME_1)
-            model_def = JuliaBUGS.BUGSExamples.VOLUME_1[m].model_def
-            data = JuliaBUGS.BUGSExamples.VOLUME_1[m].data
-            inits = JuliaBUGS.BUGSExamples.VOLUME_1[m].inits[1]
-            model = compile(model_def, data, inits)
+            m = JuliaBUGS.BUGSExamples.VOLUME_1[m]
+            model = compile(m.model_def, m.data, m.inits[1])
         end
     end
     @testset "Some corner cases" begin
@@ -98,6 +95,7 @@ else # run all
         include("cumulative_density.jl")
     end
     include("graphs.jl")
+    include("logp_tests/test_logp.jl")
     include("gibbs.jl")
     include("ext/mcmchains.jl")
 end

From 49e71ff11151346eb47cabd18ddde6ec6b24b60c Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 10:36:54 +0000
Subject: [PATCH 21/37] fix error

---
 .github/workflows/Tests.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index 9e1c33fe5..68b229edf 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -48,21 +48,21 @@ jobs:
             ${{ runner.os }}-julia-${{ matrix.version }}-
       - uses: julia-actions/julia-buildpkg@v1
       - name: Running elementary tests
-        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"unit\", \"parser\", \"analysis_passes\", \"graph\"]);"
+        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["unit", "parser", "analysis_passes", "graph"]);"
       - name: Running compilation tests
-        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"compile_BUGS_examples\", \"corner_cases\", \"logp\"]);"
+        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["compile_BUGS_examples", "corner_cases", "logp"]);"
       - name: Running `gibbs` tests
         uses: nick-fields/retry@v3
         with:
           timeout_minutes: 10
           max_attempts: 3
-          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"gibbs\"]);"
+          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["gibbs"]);"
       - name: Running `mcmchains` tests
         uses: nick-fields/retry@v3
         with:
           timeout_minutes: 10
           max_attempts: 3
-          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"mcmchains\"]);"
+          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["mcmchains"]);"
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.coverage
       - uses: codecov/codecov-action@v4

From a9862beb1f3a79d101e54ac8b9d5304c2c3d52e5 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 10:46:40 +0000
Subject: [PATCH 22/37] fix errors

---
 .github/workflows/Tests.yml | 10 ++++++----
 test/runtests.jl            | 31 ++++++++++++++++++-------------
 2 files changed, 24 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index 68b229edf..13b31fb15 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -48,21 +48,23 @@ jobs:
             ${{ runner.os }}-julia-${{ matrix.version }}-
       - uses: julia-actions/julia-buildpkg@v1
       - name: Running elementary tests
-        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["unit", "parser", "analysis_passes", "graph"]);"
+        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["--elementary"]);"
       - name: Running compilation tests
-        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["compile_BUGS_examples", "corner_cases", "logp"]);"
+        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["--compilation"]);"
+      - name: Profile compiler passes
+        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["--profile"]);"
       - name: Running `gibbs` tests
         uses: nick-fields/retry@v3
         with:
           timeout_minutes: 10
           max_attempts: 3
-          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["gibbs"]);"
+          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["--gibbs"]);"
       - name: Running `mcmchains` tests
         uses: nick-fields/retry@v3
         with:
           timeout_minutes: 10
           max_attempts: 3
-          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["mcmchains"]);"
+          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["--mcmchains"]);"
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.coverage
       - uses: codecov/codecov-action@v4
diff --git a/test/runtests.jl b/test/runtests.jl
index 171034716..49d7b541b 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -44,39 +44,44 @@ end
 
 @info "Running tests for groups: $(ARGS)"
 
-if "profile" in ARGS
-    include("profile.jl")
-elseif "unit" in ARGS
+if "--elementary" in ARGS
     @testset "Unit Tests" begin
         Documenter.doctest(JuliaBUGS; manual=false)
         include("utils.jl")
     end
-elseif "parser" in ARGS
     include("parser/test_parser.jl")
-elseif "analysis_passes" in ARGS
     include("passes.jl")
-elseif "compile_BUGS_examples" in ARGS
+    include("graphs.jl")
+end
+
+if "--compilation" in ARGS
     @testset "BUGS examples volume 1" begin
         @testset "$m" for m in keys(JuliaBUGS.BUGSExamples.VOLUME_1)
             m = JuliaBUGS.BUGSExamples.VOLUME_1[m]
             model = compile(m.model_def, m.data, m.inits[1])
         end
     end
-elseif "corner_cases" in ARGS
     @testset "Some corner cases" begin
         include("bugs_primitives.jl")
         include("compile.jl")
         include("cumulative_density.jl")
     end
-elseif "graph" in ARGS
-    include("graphs.jl")
-elseif "logp" in ARGS
     include("logp_tests/test_logp.jl")
-elseif "gibbs" in ARGS
+end
+
+if "--profile" in ARGS
+    include("profile.jl")
+end
+
+if "--gibbs" in ARGS
     include("gibbs.jl")
-elseif "mcmchains" in ARGS
+end
+
+if "--mcmchains" in ARGS
     include("ext/mcmchains.jl")
-else # run all
+end
+
+if isempty(ARGS) # run all
     @testset "Unit Tests" begin
         Documenter.doctest(JuliaBUGS; manual=false)
         include("utils.jl")

From cbe3a8cd5258e606012071c26a04a505bd97deeb Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 10:48:18 +0000
Subject: [PATCH 23/37] add escape symbol

---
 .github/workflows/Tests.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index 13b31fb15..01595bebf 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -48,11 +48,11 @@ jobs:
             ${{ runner.os }}-julia-${{ matrix.version }}-
       - uses: julia-actions/julia-buildpkg@v1
       - name: Running elementary tests
-        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["--elementary"]);"
+        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"--elementary\"]);"
       - name: Running compilation tests
-        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["--compilation"]);"
+        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"--compilation\"]);"
       - name: Profile compiler passes
-        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["--profile"]);"
+        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"--profile\"]);"
       - name: Running `gibbs` tests
         uses: nick-fields/retry@v3
         with:

From dc6f92a244443408f2560b6d9f36d214604fab0e Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 10:51:42 +0000
Subject: [PATCH 24/37] fix error

---
 test/runtests.jl | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/test/runtests.jl b/test/runtests.jl
index 49d7b541b..9e4df5c8f 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -24,16 +24,11 @@ using ReverseDiff
 AbstractMCMC.setprogress!(false)
 
 const Tests = (
-    "profile",
-    "unit",
-    "parser",
-    "analysis_passes",
-    "compile_BUGS_examples",
-    "corner_cases",
-    "graph",
-    "logp",
-    "gibbs",
-    "mcmchains",
+    "--elementary",
+    "--compilation",
+    "--profile",
+    "--gibbs",
+    "--mcmchains",
 )
 
 for arg in ARGS

From a0cc28b62f6a061f1bff58a1f7b0d47dc9b2472f Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 11:10:24 +0000
Subject: [PATCH 25/37] fix errors

---
 .github/workflows/Tests.yml | 20 ++++++++++----
 test/runtests.jl            | 54 +++++++++++--------------------------
 2 files changed, 30 insertions(+), 44 deletions(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index 01595bebf..11efbc0a6 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -48,23 +48,33 @@ jobs:
             ${{ runner.os }}-julia-${{ matrix.version }}-
       - uses: julia-actions/julia-buildpkg@v1
       - name: Running elementary tests
-        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"--elementary\"]);"
+        uses: julia-actions/julia-runtest@v1
+        env:
+          TEST_GROUP: "elementary"
       - name: Running compilation tests
-        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"--compilation\"]);"
+        uses: julia-actions/julia-runtest@v1
+        env:
+          TEST_GROUP: "compilation"
       - name: Profile compiler passes
-        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=[\"--profile\"]);"
+        uses: julia-actions/julia-runtest@v1
+        env:
+          TEST_GROUP: "profile"
       - name: Running `gibbs` tests
         uses: nick-fields/retry@v3
         with:
           timeout_minutes: 10
           max_attempts: 3
-          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["--gibbs"]);"
+          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true);"
+        env:
+          TEST_GROUP: "gibbs"
       - name: Running `mcmchains` tests
         uses: nick-fields/retry@v3
         with:
           timeout_minutes: 10
           max_attempts: 3
-          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true, test_args=["--mcmchains"]);"
+          command: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(coverage=true);"
+        env:
+          TEST_GROUP: "mcmchains"
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.coverage
       - uses: codecov/codecov-action@v4
diff --git a/test/runtests.jl b/test/runtests.jl
index 9e4df5c8f..0a98d5d76 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -24,22 +24,22 @@ using ReverseDiff
 AbstractMCMC.setprogress!(false)
 
 const Tests = (
-    "--elementary",
-    "--compilation",
-    "--profile",
-    "--gibbs",
-    "--mcmchains",
+    "elementary",
+    "compilation",
+    "profile",
+    "gibbs",
+    "mcmchains",
+    "all"
 )
 
-for arg in ARGS
-    if arg ∉ Tests
-        error("Unknown test group: $arg")
-    end
+const test_group = get(ENV, TEST_GROUP, "all")
+if test_group ∉ Tests
+    error("Unknown test group: $test_group")
 end
 
-@info "Running tests for groups: $(ARGS)"
+@info "Running tests for groups: $test_group"
 
-if "--elementary" in ARGS
+if test_group == "elementary" || test_group == "all"
     @testset "Unit Tests" begin
         Documenter.doctest(JuliaBUGS; manual=false)
         include("utils.jl")
@@ -49,7 +49,7 @@ if "--elementary" in ARGS
     include("graphs.jl")
 end
 
-if "--compilation" in ARGS
+if test_group == "compilation" || test_group == "all"
     @testset "BUGS examples volume 1" begin
         @testset "$m" for m in keys(JuliaBUGS.BUGSExamples.VOLUME_1)
             m = JuliaBUGS.BUGSExamples.VOLUME_1[m]
@@ -64,38 +64,14 @@ if "--compilation" in ARGS
     include("logp_tests/test_logp.jl")
 end
 
-if "--profile" in ARGS
+if test_group == "profile" || test_group == "all"
     include("profile.jl")
 end
 
-if "--gibbs" in ARGS
+if test_group == "gibbs" || test_group == "all"
     include("gibbs.jl")
 end
 
-if "--mcmchains" in ARGS
-    include("ext/mcmchains.jl")
-end
-
-if isempty(ARGS) # run all
-    @testset "Unit Tests" begin
-        Documenter.doctest(JuliaBUGS; manual=false)
-        include("utils.jl")
-    end
-    include("parser/test_parser.jl")
-    include("passes.jl")
-    @testset "BUGS examples volume 1" begin
-        @testset "$m" for m in keys(JuliaBUGS.BUGSExamples.VOLUME_1)
-            m = JuliaBUGS.BUGSExamples.VOLUME_1[m]
-            model = compile(m.model_def, m.data, m.inits[1])
-        end
-    end
-    @testset "Some corner cases" begin
-        include("bugs_primitives.jl")
-        include("compile.jl")
-        include("cumulative_density.jl")
-    end
-    include("graphs.jl")
-    include("logp_tests/test_logp.jl")
-    include("gibbs.jl")
+if test_group == "mcmchains" || test_group == "all"
     include("ext/mcmchains.jl")
 end

From 78230c2d867dfd1f32599daa1c8e10993f4874b3 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 11:12:55 +0000
Subject: [PATCH 26/37] fix error

---
 test/runtests.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/runtests.jl b/test/runtests.jl
index 0a98d5d76..205cb72a7 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -32,7 +32,7 @@ const Tests = (
     "all"
 )
 
-const test_group = get(ENV, TEST_GROUP, "all")
+const test_group = get(ENV, :TEST_GROUP, "all")
 if test_group ∉ Tests
     error("Unknown test group: $test_group")
 end

From 529f9897121b9e63d45387ddf3211220a70791b0 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 11:15:58 +0000
Subject: [PATCH 27/37] fix ENV key

---
 test/runtests.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/runtests.jl b/test/runtests.jl
index 205cb72a7..865d9b00b 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -32,7 +32,7 @@ const Tests = (
     "all"
 )
 
-const test_group = get(ENV, :TEST_GROUP, "all")
+const test_group = get(ENV, "TEST_GROUP", "all")
 if test_group ∉ Tests
     error("Unknown test group: $test_group")
 end

From 99712ec652c37e15077e7d725b77db4547dfa1f4 Mon Sep 17 00:00:00 2001
From: Xianda Sun <5433119+sunxd3@users.noreply.github.com>
Date: Mon, 25 Mar 2024 11:17:45 +0000
Subject: [PATCH 28/37] Update test/runtests.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 test/runtests.jl | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/test/runtests.jl b/test/runtests.jl
index 865d9b00b..8cee00ff0 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -23,14 +23,7 @@ using ReverseDiff
 
 AbstractMCMC.setprogress!(false)
 
-const Tests = (
-    "elementary",
-    "compilation",
-    "profile",
-    "gibbs",
-    "mcmchains",
-    "all"
-)
+const Tests = ("elementary", "compilation", "profile", "gibbs", "mcmchains", "all")
 
 const test_group = get(ENV, "TEST_GROUP", "all")
 if test_group ∉ Tests

From 11a60d8d0259f90a5c22668cb6387f2dfd476443 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 11:21:39 +0000
Subject: [PATCH 29/37] fix more errors

---
 test/graphs.jl | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/test/graphs.jl b/test/graphs.jl
index 43af035c0..f2d63088a 100644
--- a/test/graphs.jl
+++ b/test/graphs.jl
@@ -78,8 +78,9 @@ end
     logp += logpdf(dnorm(2.0, 1.0), 4.0) # d, where g = 2.0
     logp += logpdf(dnorm(4.0, 4.0), 5.0) # e, where h = 4.0
     logp
-end ≈ evaluate!!(model, LogDensityContext(), [-2.0, 4.0, 3.0, 2.0, 1.0, 4.0, 5.0])[2] atol =
-    1e-8
+end ≈ evaluate!!(
+    model, JuliaBUGS.LogDensityContext(), [-2.0, 4.0, 3.0, 2.0, 1.0, 4.0, 5.0]
+)[2] atol = 1e-8
 
 # AuxiliaryNodeInfo
 test_model = @bugs begin

From f057c2e463ca147706ae125b144d290a039f1d25 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 11:39:28 +0000
Subject: [PATCH 30/37] fix more errors

---
 test/graphs.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/graphs.jl b/test/graphs.jl
index f2d63088a..500c1ce61 100644
--- a/test/graphs.jl
+++ b/test/graphs.jl
@@ -65,7 +65,7 @@ mb_logp = begin
 end
 
 # order: b, l, c, a
-@test mb_logp ≈ evaluate!!(cond_model, LogDensityContext(), [c_value])[2] rtol = 1e-8
+@test mb_logp ≈ evaluate!!(cond_model, JuliaBUGS.LogDensityContext(), [c_value])[2] rtol = 1e-8
 
 # test LogDensityContext
 @test begin

From 837c6ff2446e446fff6f73f5931c78539d43ebd0 Mon Sep 17 00:00:00 2001
From: Xianda Sun <5433119+sunxd3@users.noreply.github.com>
Date: Mon, 25 Mar 2024 11:42:43 +0000
Subject: [PATCH 31/37] Update test/graphs.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 test/graphs.jl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/graphs.jl b/test/graphs.jl
index 500c1ce61..5820756e4 100644
--- a/test/graphs.jl
+++ b/test/graphs.jl
@@ -65,7 +65,8 @@ mb_logp = begin
 end
 
 # order: b, l, c, a
-@test mb_logp ≈ evaluate!!(cond_model, JuliaBUGS.LogDensityContext(), [c_value])[2] rtol = 1e-8
+@test mb_logp ≈ evaluate!!(cond_model, JuliaBUGS.LogDensityContext(), [c_value])[2] rtol =
+    1e-8
 
 # test LogDensityContext
 @test begin

From 8f22695160c4ce3a046091b2df3f4ca7dea4666f Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 11:51:40 +0000
Subject: [PATCH 32/37] fix path error

---
 test/logp_tests/test_logp.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/logp_tests/test_logp.jl b/test/logp_tests/test_logp.jl
index a6e511bb5..7a408958b 100644
--- a/test/logp_tests/test_logp.jl
+++ b/test/logp_tests/test_logp.jl
@@ -5,12 +5,12 @@ using DynamicPPL: DynamicPPL, getlogp, settrans!!, SimpleVarInfo
 @testset "Log joint probability" begin
     @testset "Single distribution models" begin
         @testset "$s" for s in [:binomial, :gamma, :lkj, :dwish, :ddirich]
-            include("./single_distribution_models/$s.jl")
+            include(joinpath(dirname(@__FILE__), "/single_distribution_models/$s.jl"))
         end
     end
     @testset "BUGS models" begin
         @testset "$s" for s in [:blockers, :bones, :dogs, :rats]
-            include("./BUGS_models/$s.jl")
+            include(joinpath(dirname(@__FILE__), "/BUGS_models/$s.jl"))
         end
     end
 end

From 6edb1537715c4e1f8e5ea68dde1115b0b240cf39 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 12:02:53 +0000
Subject: [PATCH 33/37] fix file path

---
 test/logp_tests/test_logp.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/logp_tests/test_logp.jl b/test/logp_tests/test_logp.jl
index 7a408958b..ed65eeac4 100644
--- a/test/logp_tests/test_logp.jl
+++ b/test/logp_tests/test_logp.jl
@@ -5,12 +5,12 @@ using DynamicPPL: DynamicPPL, getlogp, settrans!!, SimpleVarInfo
 @testset "Log joint probability" begin
     @testset "Single distribution models" begin
         @testset "$s" for s in [:binomial, :gamma, :lkj, :dwish, :ddirich]
-            include(joinpath(dirname(@__FILE__), "/single_distribution_models/$s.jl"))
+            include("single_distribution_models/$s.jl")
         end
     end
     @testset "BUGS models" begin
         @testset "$s" for s in [:blockers, :bones, :dogs, :rats]
-            include(joinpath(dirname(@__FILE__), "/BUGS_models/$s.jl"))
+            include("BUGS_models/$s.jl")
         end
     end
 end

From 3468be4734f3d7ba3ca24b48e8451c0347e3700b Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 12:09:42 +0000
Subject: [PATCH 34/37] fix folder name typo

---
 .../binomial.jl                                                   | 0
 .../ddirich.jl                                                    | 0
 .../dwish.jl                                                      | 0
 .../gamma.jl                                                      | 0
 .../lkj.jl                                                        | 0
 5 files changed, 0 insertions(+), 0 deletions(-)
 rename test/logp_tests/{single_distribution _models => single_distribution_models}/binomial.jl (100%)
 rename test/logp_tests/{single_distribution _models => single_distribution_models}/ddirich.jl (100%)
 rename test/logp_tests/{single_distribution _models => single_distribution_models}/dwish.jl (100%)
 rename test/logp_tests/{single_distribution _models => single_distribution_models}/gamma.jl (100%)
 rename test/logp_tests/{single_distribution _models => single_distribution_models}/lkj.jl (100%)

diff --git a/test/logp_tests/single_distribution _models/binomial.jl b/test/logp_tests/single_distribution_models/binomial.jl
similarity index 100%
rename from test/logp_tests/single_distribution _models/binomial.jl
rename to test/logp_tests/single_distribution_models/binomial.jl
diff --git a/test/logp_tests/single_distribution _models/ddirich.jl b/test/logp_tests/single_distribution_models/ddirich.jl
similarity index 100%
rename from test/logp_tests/single_distribution _models/ddirich.jl
rename to test/logp_tests/single_distribution_models/ddirich.jl
diff --git a/test/logp_tests/single_distribution _models/dwish.jl b/test/logp_tests/single_distribution_models/dwish.jl
similarity index 100%
rename from test/logp_tests/single_distribution _models/dwish.jl
rename to test/logp_tests/single_distribution_models/dwish.jl
diff --git a/test/logp_tests/single_distribution _models/gamma.jl b/test/logp_tests/single_distribution_models/gamma.jl
similarity index 100%
rename from test/logp_tests/single_distribution _models/gamma.jl
rename to test/logp_tests/single_distribution_models/gamma.jl
diff --git a/test/logp_tests/single_distribution _models/lkj.jl b/test/logp_tests/single_distribution_models/lkj.jl
similarity index 100%
rename from test/logp_tests/single_distribution _models/lkj.jl
rename to test/logp_tests/single_distribution_models/lkj.jl

From e2520f73ea567be341c57f0519dc4a24516ab2fe Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Mon, 25 Mar 2024 12:18:45 +0000
Subject: [PATCH 35/37] fix more errors

---
 test/logp_tests/test_logp.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/logp_tests/test_logp.jl b/test/logp_tests/test_logp.jl
index ed65eeac4..a6a34aec8 100644
--- a/test/logp_tests/test_logp.jl
+++ b/test/logp_tests/test_logp.jl
@@ -1,6 +1,6 @@
 using JuliaBUGS:
     BUGSGraph, DefaultContext, evaluate!!, get_params_varinfo, LogDensityContext
-using DynamicPPL: DynamicPPL, getlogp, settrans!!, SimpleVarInfo
+using DynamicPPL: DynamicPPL, getlogp, settrans!!, SimpleVarInfo, @model
 
 @testset "Log joint probability" begin
     @testset "Single distribution models" begin

From 20b083fff9394a4b903420e1dafaa7fa936108f0 Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Tue, 26 Mar 2024 09:36:13 +0000
Subject: [PATCH 36/37] output profile result to step summary

---
 .github/workflows/Tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index 11efbc0a6..32c987ef3 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -56,7 +56,7 @@ jobs:
         env:
           TEST_GROUP: "compilation"
       - name: Profile compiler passes
-        uses: julia-actions/julia-runtest@v1
+        run: julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.test(;coverage=true);" >> $GITHUB_STEP_SUMMARY
         env:
           TEST_GROUP: "profile"
       - name: Running `gibbs` tests

From 224d3a64b827204d4a66fb00a7e5ec401804a3fb Mon Sep 17 00:00:00 2001
From: Xianda Sun <sunxdt@gmail.com>
Date: Tue, 26 Mar 2024 09:39:34 +0000
Subject: [PATCH 37/37] remove CACHE_NAME from env

---
 .github/workflows/Tests.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
index 32c987ef3..99f553b42 100644
--- a/.github/workflows/Tests.yml
+++ b/.github/workflows/Tests.yml
@@ -29,8 +29,6 @@ jobs:
             os: ubuntu-latest
             arch: x64
             coverage: true
-    env:
-      CACHE_NAME: julia-${{ matrix.version }}-${{ matrix.arch }}
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
@@ -42,9 +40,9 @@ jobs:
           path: |
             ~/.julia
             ~/.julia/artifacts
-          key: ${{ runner.os }}-${{ env.CACHE_NAME }}-${{ hashFiles('**/Project.toml', '**/Manifest.toml') }}
+          key: ${{ runner.os }}-julia-${{ matrix.version }}-${{ matrix.arch }}-${{ hashFiles('**/Project.toml', '**/Manifest.toml') }}
           restore-keys: |
-            ${{ runner.os }}-${{ env.CACHE_NAME }}-
+            ${{ runner.os }}-julia-${{ matrix.version }}-${{ matrix.arch }}-
             ${{ runner.os }}-julia-${{ matrix.version }}-
       - uses: julia-actions/julia-buildpkg@v1
       - name: Running elementary tests