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Merge branch 'development' into rm_language_suffix
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‎.clang-tidy

+7-3
Original file line numberDiff line numberDiff line change
@@ -6,21 +6,25 @@ Checks: >
66
clang-diagnostic-*,
77
cppcoreguidelines-*,
88
-cppcoreguidelines-avoid-c-arrays,
9-
-cppcoreguidelines-avoid-goto,
109
-cppcoreguidelines-avoid-magic-numbers,
1110
-cppcoreguidelines-avoid-non-const-global-variables,
1211
-cppcoreguidelines-init-variables,
1312
-cppcoreguidelines-interfaces-global-init,
1413
-cppcoreguidelines-macro-usage,
15-
-cppcoreguidelines-no-malloc,
1614
-cppcoreguidelines-non-private-member-variables-in-classes,
1715
-cppcoreguidelines-owning-memory,
1816
-cppcoreguidelines-pro-*,
17+
misc-*,
18+
-misc-const-correctness,
19+
-misc-include-cleaner,
20+
-misc-non-private-member-variables-in-classes,
21+
-misc-use-anonymous-namespace,
1922
modernize-*,
2023
-modernize-avoid-c-arrays,
2124
-modernize-use-trailing-return-type,
22-
-modernize-use-using,
2325
performance-*,
26+
-performance-avoid-endl,
27+
portability-*,
2428
readability-*,
2529
-readability-avoid-const-params-in-decls,
2630
-readability-braces-around-statements,

‎.editorconfig

+62
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@@ -0,0 +1,62 @@
1+
# http://EditorConfig.org
2+
#
3+
# precedence of rules is bottom to top
4+
5+
# this is the top-most EditorConfig file
6+
root = true
7+
8+
9+
[*.{c,h,cpp,hpp,H,py}]
10+
# 4 space indentation
11+
indent_style = space
12+
indent_size = 4
13+
14+
# Clean up trailing whitespace
15+
trim_trailing_whitespace = true
16+
17+
# unix-style newlines
18+
end_of_line = lf
19+
20+
# newline ending in files
21+
insert_final_newline = true
22+
23+
[networks/**/reaclib_rates.H]
24+
# some reaclib rate labels have trailing spaces
25+
trim_trailing_whitespace = false
26+
27+
28+
[*.md]
29+
# two end of line whitespaces are newlines without a paragraph
30+
trim_trailing_whitespace = false
31+
32+
33+
[*.rst]
34+
# Enforce UTF-8 encoding
35+
charset = utf-8
36+
37+
# Unix-style newlines
38+
end_of_line = lf
39+
40+
# Newline ending in files
41+
insert_final_newline = true
42+
43+
# 3 space indentation
44+
indent_style = space
45+
indent_size = 3
46+
47+
# Clean up trailing whitespace
48+
trim_trailing_whitespace = true
49+
50+
[{Makefile,GNUmakefile,Make.*}]
51+
# TABs are part of its syntax
52+
indent_style = tab
53+
indent_size = unset
54+
55+
56+
[util/gcem/**]
57+
# don't mess with the gcem subtree
58+
indent_style = unset
59+
indent_size = unset
60+
trim_trailing_whitespace = unset
61+
end_of_line = unset
62+
insert_final_newline = unset

‎.git-blame-ignore-revs

+2
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@@ -0,0 +1,2 @@
1+
# Replaced tabs with spaces and trimmed trailing whitespace
2+
5a2247f598f88f80ad8b186188fccfd5537b18d3

‎.github/dependabot.yml

+16
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
1+
# Dependabot configuration
2+
# ref: https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/configuration-options-for-dependency-updates
3+
version: 2
4+
updates:
5+
- package-ecosystem: "github-actions"
6+
directory: "/"
7+
schedule:
8+
interval: "weekly"
9+
target-branch: "development"
10+
11+
- package-ecosystem: "pip"
12+
directory: "/"
13+
schedule:
14+
interval: "weekly"
15+
target-branch: "development"
16+

‎.github/workflows/burn_cell.yml

+8-8
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ jobs:
55
burn_cell:
66
runs-on: ubuntu-latest
77
steps:
8-
- uses: actions/checkout@v3
8+
- uses: actions/checkout@v4
99
with:
1010
fetch-depth: 0
1111

@@ -40,7 +40,7 @@ jobs:
4040
- name: Compare to stored output (VODE, subch_approx)
4141
run: |
4242
cd unit_test/burn_cell
43-
diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/subch_approx_unit_test.out
43+
diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/subch_approx_unit_test.out
4444
4545
- name: Compile, burn_cell (VODE, ECSN)
4646
run: |
@@ -56,7 +56,7 @@ jobs:
5656
- name: Compare to stored output (VODE, ECSN)
5757
run: |
5858
cd unit_test/burn_cell
59-
diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/ecsn_unit_test.out
59+
diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/ecsn_unit_test.out
6060
6161
- name: Compile, burn_cell (VODE, ignition_chamulak)
6262
run: |
@@ -72,7 +72,7 @@ jobs:
7272
- name: Compare to stored output (VODE, ignition_chamulak)
7373
run: |
7474
cd unit_test/burn_cell
75-
diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/chamulak_VODE_unit_test.out
75+
diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/chamulak_VODE_unit_test.out
7676
7777
- name: Compile, burn_cell (ForwardEuler, triple_alpha_plus_cago)
7878
run: |
@@ -88,7 +88,7 @@ jobs:
8888
- name: Compare to stored output (ForwardEuler, triple_alpha_plus_cago)
8989
run: |
9090
cd unit_test/burn_cell
91-
diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/triple_alpha_plus_cago_FE_unit_test.out
91+
diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/triple_alpha_plus_cago_FE_unit_test.out
9292
9393
- name: Compile, burn_cell (BackwardEuler, subch_approx)
9494
run: |
@@ -104,7 +104,7 @@ jobs:
104104
- name: Compare to stored output (BackwardEuler, subch_approx)
105105
run: |
106106
cd unit_test/burn_cell
107-
diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/subch_approx_BE_unit_test.out
107+
diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/subch_approx_BE_unit_test.out
108108
109109
- name: Compile, burn_cell (QSS, aprox13)
110110
run: |
@@ -120,7 +120,7 @@ jobs:
120120
- name: Compare to stored output (QSS, aprox13)
121121
run: |
122122
cd unit_test/burn_cell
123-
diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/aprox13_QSS_unit_test.out
123+
diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/aprox13_QSS_unit_test.out
124124
125125
- name: Compile, burn_cell (RKC, aprox13)
126126
run: |
@@ -136,4 +136,4 @@ jobs:
136136
- name: Compare to stored output (RKC, aprox13)
137137
run: |
138138
cd unit_test/burn_cell
139-
diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/aprox13_RKC_unit_test.out
139+
diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/aprox13_RKC_unit_test.out

‎.github/workflows/burn_cell_primordial_chem.yml

+2-2
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ jobs:
77
runs-on: ubuntu-latest
88

99
steps:
10-
- uses: actions/checkout@v3
10+
- uses: actions/checkout@v4
1111
with:
1212
fetch-depth: 0
1313

@@ -47,7 +47,7 @@ jobs:
4747
value2=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution.out)
4848
4949
difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }')
50-
50+
5151
if (( $(echo "$difference > $threshold" | bc -l) )); then
5252
echo "Line number: $line_number"
5353
echo "Value in test.out: $value1"

‎.github/workflows/burn_cell_sdc.yml

+17-1
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ jobs:
55
burn_cell_sdc:
66
runs-on: ubuntu-latest
77
steps:
8-
- uses: actions/checkout@v3
8+
- uses: actions/checkout@v4
99
with:
1010
fetch-depth: 0
1111

@@ -58,3 +58,19 @@ jobs:
5858
cd unit_test/burn_cell_sdc
5959
diff state_over_time.txt ci-benchmarks/aprox19_BE_state_over_time.txt
6060
61+
- name: Compile, burn_cell_sdc (RKC, aprox19)
62+
run: |
63+
cd unit_test/burn_cell_sdc
64+
make realclean
65+
make INTEGRATOR_DIR=RKC NETWORK_DIR=aprox19 -j 4
66+
67+
- name: Run burn_cell_sdc (RKC, aprox19)
68+
run: |
69+
cd unit_test/burn_cell_sdc
70+
./main3d.gnu.ex inputs_aprox19.ci
71+
72+
- name: Compare to stored output (RKC, aprox19)
73+
run: |
74+
cd unit_test/burn_cell_sdc
75+
diff state_over_time.txt ci-benchmarks/aprox19_RKC_state_over_time.txt
76+

‎.github/workflows/c-linter.yml

+6-9
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ jobs:
66
cpp-linter:
77
runs-on: ubuntu-latest
88
steps:
9-
- uses: actions/checkout@v3
9+
- uses: actions/checkout@v4
1010
with:
1111
fetch-depth: 0
1212

@@ -22,28 +22,25 @@ jobs:
2222
if [[ -n "${AMREX_HOME}" ]]; then exit 1; fi
2323
cd ../..
2424
25-
- name: Install dependencies
26-
run: |
27-
sudo apt-get update -y -qq
28-
sudo apt-get -qq -y install curl clang-tidy cmake jq clang cppcheck clang-format bear g++>=9.3.0
29-
3025
- name: Run cpp linter
3126
uses: AMReX-Astro/cpp-linter-action@main
3227
with:
3328
build_path: 'unit_test/test_react'
3429
make_options: '-j 2 USE_OMP=FALSE USE_MPI=FALSE USE_CUDA=FALSE DEBUG=TRUE'
35-
ignore_files: 'amrex'
30+
ignore_files: 'amrex|util/gcem'
3631
header_filter: '(/conductivity/|/constants/|/EOS/|/integration/|/interfaces/|/networks/|/neutrinos/|/nse_solver/|/opacity/|/rates/|/screening/|/util/|^\./).*\.H$'
3732
config_file: ${GITHUB_WORKSPACE}/.clang-tidy
33+
# not sure why cppcheck tests _MSC_VER, since it's only referenced from gcem
34+
cppcheck_options: '-U_OPENMP -UAMREX_USE_GPU -UAMREX_USE_CUDA -UAMREX_USE_HIP -U_MSC_VER'
3835

3936
- name: Archive clang tidy report
40-
uses: actions/upload-artifact@v1
37+
uses: actions/upload-artifact@v4
4138
with:
4239
name: clang-tidy-report
4340
path: clang-tidy-report.txt
4441

4542
- name: Archive cppcheck report
46-
uses: actions/upload-artifact@v1
43+
uses: actions/upload-artifact@v4
4744
with:
4845
name: cppcheck-report
4946
path: cppcheck-report.txt

‎.github/workflows/castro-development.yml

+85
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,85 @@
1+
name: Castro development
2+
3+
on: [push, pull_request]
4+
5+
concurrency:
6+
group: ${{ github.ref }}-${{ github.head_ref }}-apps-dev
7+
cancel-in-progress: true
8+
9+
jobs:
10+
castro-development:
11+
name: Castro development
12+
runs-on: ubuntu-latest
13+
steps:
14+
- uses: actions/checkout@v4
15+
- name: Download Castro
16+
uses: actions/checkout@v4
17+
with:
18+
repository: 'AMReX-Astro/Castro'
19+
ref: development
20+
path: 'Castro'
21+
- name: Download AMReX
22+
uses: actions/checkout@v4
23+
with:
24+
repository: 'AMReX-Codes/amrex'
25+
ref: development
26+
path: 'amrex'
27+
- name: Dependencies
28+
run: |
29+
.github/workflows/dependencies/dependencies.sh
30+
.github/workflows/dependencies/dependencies_ccache.sh
31+
- name: Set Up Cache
32+
uses: actions/cache@v4
33+
with:
34+
path: ~/.cache/ccache
35+
key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
36+
restore-keys: |
37+
ccache-${{ github.workflow }}-${{ github.job }}-git-
38+
- name: Build flame_wave
39+
run: |
40+
export CCACHE_COMPRESS=1
41+
export CCACHE_COMPRESSLEVEL=10
42+
export CCACHE_MAXSIZE=75M
43+
export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
44+
ccache -z
45+
46+
export AMREX_HOME=${PWD}/amrex
47+
export MICROPHYSICS_HOME=${PWD}
48+
49+
cd Castro/Exec/science/flame_wave/
50+
make -j2 CCACHE=ccache USE_MPI=FALSE
51+
52+
ccache -s
53+
du -hs ~/.cache/ccache
54+
55+
- name: Build subchandra
56+
run: |
57+
export CCACHE_COMPRESS=1
58+
export CCACHE_COMPRESSLEVEL=10
59+
export CCACHE_MAXSIZE=75M
60+
export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
61+
ccache -z
62+
63+
export AMREX_HOME=${PWD}/amrex
64+
export MICROPHYSICS_HOME=${PWD}
65+
66+
cd Castro/Exec/science/subchandra/
67+
make -j2 CCACHE=ccache USE_MPI=FALSE
68+
69+
ccache -s
70+
du -hs ~/.cache/ccache
71+
72+
save_pr_number:
73+
if: github.event_name == 'pull_request'
74+
runs-on: ubuntu-latest
75+
steps:
76+
- name: Save PR number
77+
env:
78+
PR_NUMBER: ${{ github.event.number }}
79+
run: |
80+
echo $PR_NUMBER > pr_number.txt
81+
- uses: actions/upload-artifact@v4
82+
with:
83+
name: pr_number
84+
path: pr_number.txt
85+
retention-days: 1

‎.github/workflows/castro.yml

+5-5
Original file line numberDiff line numberDiff line change
@@ -11,19 +11,19 @@ jobs:
1111
name: Castro
1212
runs-on: ubuntu-latest
1313
steps:
14-
- uses: actions/checkout@v3
14+
- uses: actions/checkout@v4
1515
- name: Get Latest Release Tag
1616
run: |
1717
AMREX_TAG=$(wget https://github.com/AMReX-Codes/amrex/releases/latest 2>&1 | grep Location: | awk '{print $2}' | awk -F/ '{print $NF}')
1818
echo "AMREX_TAG=$AMREX_TAG" >> $GITHUB_ENV
1919
- name: Download Castro
20-
uses: actions/checkout@v3
20+
uses: actions/checkout@v4
2121
with:
2222
repository: 'AMReX-Astro/Castro'
2323
ref: development
2424
path: 'Castro'
2525
- name: Download AMReX
26-
uses: actions/checkout@v3
26+
uses: actions/checkout@v4
2727
with:
2828
repository: 'AMReX-Codes/amrex'
2929
ref: ${{env.AMREX_TAG}}
@@ -33,7 +33,7 @@ jobs:
3333
.github/workflows/dependencies/dependencies.sh
3434
.github/workflows/dependencies/dependencies_ccache.sh
3535
- name: Set Up Cache
36-
uses: actions/cache@v3
36+
uses: actions/cache@v4
3737
with:
3838
path: ~/.cache/ccache
3939
key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
@@ -82,7 +82,7 @@ jobs:
8282
PR_NUMBER: ${{ github.event.number }}
8383
run: |
8484
echo $PR_NUMBER > pr_number.txt
85-
- uses: actions/upload-artifact@v3
85+
- uses: actions/upload-artifact@v4
8686
with:
8787
name: pr_number
8888
path: pr_number.txt

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