Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

mambaforge is depricated and need miniforge for action builds #181

Merged
merged 9 commits into from
Nov 10, 2024
Merged

mambaforge is depricated and need miniforge for action builds #181

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
5f2eec8
mambaforge is depricated and need miniforge for action builds
Acribbs Nov 10, 2024
b5a97d9
Revert "mambaforge is depricated and need miniforge for action builds"
Acribbs Nov 10, 2024
06cdd31
github actions didnt pick up my previous file, attempted to only chan…
Acribbs Nov 10, 2024
2470db5
try v1 of miniconda setup
Acribbs Nov 10, 2024
310c0b3
specify the url link
Acribbs Nov 10, 2024
2767d85
made changes to file paths
Acribbs Nov 10, 2024
b3cef0e
cleaned up yml and remove issues
Acribbs Nov 10, 2024
64da955
oops forgot to make it work with osx
Acribbs Nov 10, 2024
9542a1b
default cpu when value is not integer
Acribbs Nov 10, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 12 additions & 4 deletions .github/workflows/cgatcore_python.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,17 +26,25 @@ jobs:
CACHE_NUMBER: 0
with:
path: ~/conda_pkgs_dir
key:
${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
hashFiles('conda/environments/cgat-core.yml') }}
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda/environments/cgat-core.yml') }}
- name: Set installer URL
id: set-installer-url
run: |
if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
echo "installer-url=https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" >> $GITHUB_ENV
elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then
echo "installer-url=https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh" >> $GITHUB_ENV
fi
- uses: conda-incubator/setup-miniconda@v2
with:
installer-url: ${{ env.installer-url }}
python-version: ${{ matrix.python-version }}
channels: conda-forge, bioconda, defaults
channel-priority: true
activate-environment: cgat-core
environment-file: conda/environments/cgat-core.yml
miniforge-variant: Mambaforge
- name: Configure Conda Paths
run: echo "/usr/share/miniconda3/condabin" >> $GITHUB_PATH
- name: Show conda
run: |
conda info
Expand Down
12 changes: 9 additions & 3 deletions cgatcore/pipeline/execution.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1038,10 +1038,16 @@ def _convert(key, v):
data.update(dict([(x[0], _convert(x[0], x[1]))
for x in pairs if len(x) == 2]))

# remove % sign
cpu_value = data.get("percent_cpu", "0")
# Strip potential '%' symbols, handle non-numeric cases gracefully
try:
percent_cpu = int(re.sub("%", "", cpu_value)) if cpu_value.replace("%", "").strip().isdigit() else 0
except ValueError:
percent_cpu = 0 # Default or fallback value, adjust as necessary

data.update(
{"percent_cpu": int(re.sub("%", "", data.get("percent_cpu", 0))),
"cpu_t": float(data["user_t"]) + float(data["sys_t"])})
{"percent_cpu": percent_cpu,
"cpu_t": float(data.get("user_t", 0)) + float(data.get("sys_t", 0))})

return JobInfo(jobId=process.pid, resourceUsage=data)

Expand Down
Loading