From edbdaaaca8543f62fc2716620a044f663d29b26f Mon Sep 17 00:00:00 2001 From: munishchouhan Date: Thu, 25 Jun 2026 16:19:10 +0200 Subject: [PATCH 1/2] Use conda-lock to generate environment.lock so pip deps are included MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The current templates run `micromamba env export --name base --explicit` which silently omits any `pip:` entries from environment.yml, so users with mixed conda+pip environments get incomplete lock files. Switch the lockfile generation step in the conda-file templates (v1 and v2, dockerfile and singularity) to install `conda-lock` and invoke it against the user's conda.yml. The actual `micromamba install` step that builds the image is left unchanged, so image contents are produced exactly as before — conda-lock is used only to render the lockfile. Closes #975 Co-Authored-By: Claude Opus 4.7 (1M context) --- .../dockerfile-conda-file.txt | 3 ++- .../singularityfile-conda-file.txt | 3 ++- .../dockerfile-conda-file.txt | 3 ++- .../singularityfile-conda-file.txt | 3 ++- .../wave/util/ContainerHelperTest.groovy | 15 ++++++++---- .../seqera/wave/util/TemplateUtilsTest.groovy | 24 ++++++++++++------- 6 files changed, 34 insertions(+), 17 deletions(-) diff --git a/src/main/resources/templates/conda-micromamba-v1/dockerfile-conda-file.txt b/src/main/resources/templates/conda-micromamba-v1/dockerfile-conda-file.txt index 7ca63ccec7..6811feaa0a 100644 --- a/src/main/resources/templates/conda-micromamba-v1/dockerfile-conda-file.txt +++ b/src/main/resources/templates/conda-micromamba-v1/dockerfile-conda-file.txt @@ -2,7 +2,8 @@ FROM {{base_image}} COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml RUN micromamba install -y -n base -f /tmp/conda.yml \ {{base_packages}} - && micromamba env export --name base --explicit > environment.lock \ + && micromamba install -y -n base conda-forge::conda-lock \ + && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \ && echo ">> CONDA_LOCK_START" \ && cat environment.lock \ && echo "<< CONDA_LOCK_END" \ diff --git a/src/main/resources/templates/conda-micromamba-v1/singularityfile-conda-file.txt b/src/main/resources/templates/conda-micromamba-v1/singularityfile-conda-file.txt index 08eb6d529c..4d02651d0d 100644 --- a/src/main/resources/templates/conda-micromamba-v1/singularityfile-conda-file.txt +++ b/src/main/resources/templates/conda-micromamba-v1/singularityfile-conda-file.txt @@ -5,7 +5,8 @@ From: {{base_image}} %post micromamba install -y -n base -f /scratch/conda.yml {{base_packages}} - micromamba env export --name base --explicit > environment.lock + micromamba install -y -n base conda-forge::conda-lock + conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock echo ">> CONDA_LOCK_START" cat environment.lock echo "<< CONDA_LOCK_END" diff --git a/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt b/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt index 05a980b572..1c88609069 100644 --- a/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt +++ b/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt @@ -5,8 +5,9 @@ RUN (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \ || (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \ && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \ {{base_packages}} + && micromamba install -y -n base conda-forge::conda-lock \ + && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \ && micromamba clean -a -y \ - && micromamba env export --name base --explicit > environment.lock \ && echo ">> CONDA_LOCK_START" \ && cat environment.lock \ && echo "<< CONDA_LOCK_END" diff --git a/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt b/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt index a5ab35211e..052f7b7f92 100644 --- a/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt +++ b/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt @@ -8,8 +8,9 @@ From: {{mamba_image}} || (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \ && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /scratch/conda.yml) {{base_packages}} + micromamba install -y -n base conda-forge::conda-lock + conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock micromamba clean -a -y - micromamba env export --name base --explicit > environment.lock echo ">> CONDA_LOCK_START" cat environment.lock echo "<< CONDA_LOCK_END" diff --git a/src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy b/src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy index 087669f1cc..3244efe707 100644 --- a/src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy +++ b/src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy @@ -123,7 +123,8 @@ class ContainerHelperTest extends Specification { %post micromamba install -y -n base -f /scratch/conda.yml micromamba install -y -n base foo::one bar::two - micromamba env export --name base --explicit > environment.lock + micromamba install -y -n base conda-forge::conda-lock + conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock echo ">> CONDA_LOCK_START" cat environment.lock echo "<< CONDA_LOCK_END" @@ -150,7 +151,8 @@ class ContainerHelperTest extends Specification { COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml RUN micromamba install -y -n base -f /tmp/conda.yml \\ && micromamba install -y -n base foo::one bar::two \\ - && micromamba env export --name base --explicit > environment.lock \\ + && micromamba install -y -n base conda-forge::conda-lock \\ + && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ && echo "<< CONDA_LOCK_END" \\ @@ -736,8 +738,9 @@ class ContainerHelperTest extends Specification { || (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\ && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\ && micromamba install -y -n base conda-forge::procps-ng \\ + && micromamba install -y -n base conda-forge::conda-lock \\ + && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && micromamba clean -a -y \\ - && micromamba env export --name base --explicit > environment.lock \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ && echo "<< CONDA_LOCK_END" @@ -774,8 +777,9 @@ class ContainerHelperTest extends Specification { || (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\ && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\ && micromamba install -y -n base conda-forge::procps-ng \\ + && micromamba install -y -n base conda-forge::conda-lock \\ + && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && micromamba clean -a -y \\ - && micromamba env export --name base --explicit > environment.lock \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ && echo "<< CONDA_LOCK_END" @@ -817,8 +821,9 @@ class ContainerHelperTest extends Specification { || (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\ && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\ && micromamba install -y -n base foo::one bar::two \\ + && micromamba install -y -n base conda-forge::conda-lock \\ + && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && micromamba clean -a -y \\ - && micromamba env export --name base --explicit > environment.lock \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ && echo "<< CONDA_LOCK_END" diff --git a/src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy b/src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy index eb3f3d1252..7e761e6502 100644 --- a/src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy +++ b/src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy @@ -37,7 +37,8 @@ class TemplateUtilsTest extends Specification { COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml RUN micromamba install -y -n base -f /tmp/conda.yml \\ && micromamba install -y -n base foo::bar \\ - && micromamba env export --name base --explicit > environment.lock \\ + && micromamba install -y -n base conda-forge::conda-lock \\ + && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ && echo "<< CONDA_LOCK_END" \\ @@ -55,7 +56,8 @@ class TemplateUtilsTest extends Specification { COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml RUN micromamba install -y -n base -f /tmp/conda.yml \\ && micromamba install -y -n base conda-forge::procps-ng \\ - && micromamba env export --name base --explicit > environment.lock \\ + && micromamba install -y -n base conda-forge::conda-lock \\ + && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ && echo "<< CONDA_LOCK_END" \\ @@ -196,7 +198,8 @@ class TemplateUtilsTest extends Specification { %post micromamba install -y -n base -f /scratch/conda.yml micromamba install -y -n base foo::bar=1.0 - micromamba env export --name base --explicit > environment.lock + micromamba install -y -n base conda-forge::conda-lock + conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock echo ">> CONDA_LOCK_START" cat environment.lock echo "<< CONDA_LOCK_END" @@ -217,7 +220,8 @@ class TemplateUtilsTest extends Specification { %post micromamba install -y -n base -f /scratch/conda.yml micromamba install -y -n base conda-forge::procps-ng - micromamba env export --name base --explicit > environment.lock + micromamba install -y -n base conda-forge::conda-lock + conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock echo ">> CONDA_LOCK_START" cat environment.lock echo "<< CONDA_LOCK_END" @@ -488,8 +492,9 @@ class TemplateUtilsTest extends Specification { || (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\ && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\ && micromamba install -y -n base conda-forge::procps-ng \\ + && micromamba install -y -n base conda-forge::conda-lock \\ + && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && micromamba clean -a -y \\ - && micromamba env export --name base --explicit > environment.lock \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ && echo "<< CONDA_LOCK_END" @@ -513,8 +518,9 @@ class TemplateUtilsTest extends Specification { || (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\ && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\ && micromamba install -y -n base conda-forge::procps-ng \\ + && micromamba install -y -n base conda-forge::conda-lock \\ + && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && micromamba clean -a -y \\ - && micromamba env export --name base --explicit > environment.lock \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ && echo "<< CONDA_LOCK_END" @@ -774,8 +780,9 @@ class TemplateUtilsTest extends Specification { || (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\ && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /scratch/conda.yml) micromamba install -y -n base conda-forge::procps-ng + micromamba install -y -n base conda-forge::conda-lock + conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock micromamba clean -a -y - micromamba env export --name base --explicit > environment.lock echo ">> CONDA_LOCK_START" cat environment.lock echo "<< CONDA_LOCK_END" @@ -799,8 +806,9 @@ class TemplateUtilsTest extends Specification { || (cat /tmp/mamba.log >&2 && grep -q __cuda /tmp/mamba.log \\ && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /scratch/conda.yml) micromamba install -y -n base conda-forge::procps-ng + micromamba install -y -n base conda-forge::conda-lock + conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock micromamba clean -a -y - micromamba env export --name base --explicit > environment.lock echo ">> CONDA_LOCK_START" cat environment.lock echo "<< CONDA_LOCK_END" From d9b48c9d55d4fa100a9e351053dbabbae96a03cb Mon Sep 17 00:00:00 2001 From: munishchouhan Date: Thu, 25 Jun 2026 17:11:23 +0200 Subject: [PATCH 2/2] Invoke conda-lock via `micromamba run -n base` The conda-lock binary lives at /opt/conda/bin/conda-lock after the `micromamba install conda-forge::conda-lock` step, but /opt/conda/bin is not on PATH inside the mambaorg/micromamba build stage. The previous template invoked `conda-lock ...` directly and failed with `bash: line 1: conda-lock: command not found` (exit 127). Run it via `micromamba run -n base` instead so the base env's PATH is resolved correctly. Co-Authored-By: Claude Opus 4.7 (1M context) --- .../dockerfile-conda-file.txt | 2 +- .../singularityfile-conda-file.txt | 2 +- .../dockerfile-conda-file.txt | 2 +- .../singularityfile-conda-file.txt | 2 +- .../seqera/wave/util/ContainerHelperTest.groovy | 10 +++++----- .../io/seqera/wave/util/TemplateUtilsTest.groovy | 16 ++++++++-------- 6 files changed, 17 insertions(+), 17 deletions(-) diff --git a/src/main/resources/templates/conda-micromamba-v1/dockerfile-conda-file.txt b/src/main/resources/templates/conda-micromamba-v1/dockerfile-conda-file.txt index 6811feaa0a..8da044c6f1 100644 --- a/src/main/resources/templates/conda-micromamba-v1/dockerfile-conda-file.txt +++ b/src/main/resources/templates/conda-micromamba-v1/dockerfile-conda-file.txt @@ -3,7 +3,7 @@ COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml RUN micromamba install -y -n base -f /tmp/conda.yml \ {{base_packages}} && micromamba install -y -n base conda-forge::conda-lock \ - && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \ + && micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \ && echo ">> CONDA_LOCK_START" \ && cat environment.lock \ && echo "<< CONDA_LOCK_END" \ diff --git a/src/main/resources/templates/conda-micromamba-v1/singularityfile-conda-file.txt b/src/main/resources/templates/conda-micromamba-v1/singularityfile-conda-file.txt index 4d02651d0d..24be3fe7a2 100644 --- a/src/main/resources/templates/conda-micromamba-v1/singularityfile-conda-file.txt +++ b/src/main/resources/templates/conda-micromamba-v1/singularityfile-conda-file.txt @@ -6,7 +6,7 @@ From: {{base_image}} micromamba install -y -n base -f /scratch/conda.yml {{base_packages}} micromamba install -y -n base conda-forge::conda-lock - conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock + micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock echo ">> CONDA_LOCK_START" cat environment.lock echo "<< CONDA_LOCK_END" diff --git a/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt b/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt index 1c88609069..7d5e9dbb57 100644 --- a/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt +++ b/src/main/resources/templates/conda-micromamba-v2/dockerfile-conda-file.txt @@ -6,7 +6,7 @@ RUN (micromamba install -y -n base -f /tmp/conda.yml > /tmp/mamba.log 2>&1 \ && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \ {{base_packages}} && micromamba install -y -n base conda-forge::conda-lock \ - && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \ + && micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \ && micromamba clean -a -y \ && echo ">> CONDA_LOCK_START" \ && cat environment.lock \ diff --git a/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt b/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt index 052f7b7f92..74bc9114b7 100644 --- a/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt +++ b/src/main/resources/templates/conda-micromamba-v2/singularityfile-conda-file.txt @@ -9,7 +9,7 @@ From: {{mamba_image}} && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /scratch/conda.yml) {{base_packages}} micromamba install -y -n base conda-forge::conda-lock - conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock + micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock micromamba clean -a -y echo ">> CONDA_LOCK_START" cat environment.lock diff --git a/src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy b/src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy index 3244efe707..46338cefbe 100644 --- a/src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy +++ b/src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy @@ -124,7 +124,7 @@ class ContainerHelperTest extends Specification { micromamba install -y -n base -f /scratch/conda.yml micromamba install -y -n base foo::one bar::two micromamba install -y -n base conda-forge::conda-lock - conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock + micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock echo ">> CONDA_LOCK_START" cat environment.lock echo "<< CONDA_LOCK_END" @@ -152,7 +152,7 @@ class ContainerHelperTest extends Specification { RUN micromamba install -y -n base -f /tmp/conda.yml \\ && micromamba install -y -n base foo::one bar::two \\ && micromamba install -y -n base conda-forge::conda-lock \\ - && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ + && micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ && echo "<< CONDA_LOCK_END" \\ @@ -739,7 +739,7 @@ class ContainerHelperTest extends Specification { && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\ && micromamba install -y -n base conda-forge::procps-ng \\ && micromamba install -y -n base conda-forge::conda-lock \\ - && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ + && micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && micromamba clean -a -y \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ @@ -778,7 +778,7 @@ class ContainerHelperTest extends Specification { && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\ && micromamba install -y -n base conda-forge::procps-ng \\ && micromamba install -y -n base conda-forge::conda-lock \\ - && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ + && micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && micromamba clean -a -y \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ @@ -822,7 +822,7 @@ class ContainerHelperTest extends Specification { && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\ && micromamba install -y -n base foo::one bar::two \\ && micromamba install -y -n base conda-forge::conda-lock \\ - && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ + && micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && micromamba clean -a -y \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ diff --git a/src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy b/src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy index 7e761e6502..97ec7b6c29 100644 --- a/src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy +++ b/src/test/groovy/io/seqera/wave/util/TemplateUtilsTest.groovy @@ -38,7 +38,7 @@ class TemplateUtilsTest extends Specification { RUN micromamba install -y -n base -f /tmp/conda.yml \\ && micromamba install -y -n base foo::bar \\ && micromamba install -y -n base conda-forge::conda-lock \\ - && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ + && micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ && echo "<< CONDA_LOCK_END" \\ @@ -57,7 +57,7 @@ class TemplateUtilsTest extends Specification { RUN micromamba install -y -n base -f /tmp/conda.yml \\ && micromamba install -y -n base conda-forge::procps-ng \\ && micromamba install -y -n base conda-forge::conda-lock \\ - && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ + && micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ && echo "<< CONDA_LOCK_END" \\ @@ -199,7 +199,7 @@ class TemplateUtilsTest extends Specification { micromamba install -y -n base -f /scratch/conda.yml micromamba install -y -n base foo::bar=1.0 micromamba install -y -n base conda-forge::conda-lock - conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock + micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock echo ">> CONDA_LOCK_START" cat environment.lock echo "<< CONDA_LOCK_END" @@ -221,7 +221,7 @@ class TemplateUtilsTest extends Specification { micromamba install -y -n base -f /scratch/conda.yml micromamba install -y -n base conda-forge::procps-ng micromamba install -y -n base conda-forge::conda-lock - conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock + micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock echo ">> CONDA_LOCK_START" cat environment.lock echo "<< CONDA_LOCK_END" @@ -493,7 +493,7 @@ class TemplateUtilsTest extends Specification { && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\ && micromamba install -y -n base conda-forge::procps-ng \\ && micromamba install -y -n base conda-forge::conda-lock \\ - && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ + && micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && micromamba clean -a -y \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ @@ -519,7 +519,7 @@ class TemplateUtilsTest extends Specification { && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /tmp/conda.yml)) \\ && micromamba install -y -n base conda-forge::procps-ng \\ && micromamba install -y -n base conda-forge::conda-lock \\ - && conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ + && micromamba run -n base conda-lock --file /tmp/conda.yml --platform linux-64 --lockfile environment.lock \\ && micromamba clean -a -y \\ && echo ">> CONDA_LOCK_START" \\ && cat environment.lock \\ @@ -781,7 +781,7 @@ class TemplateUtilsTest extends Specification { && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /scratch/conda.yml) micromamba install -y -n base conda-forge::procps-ng micromamba install -y -n base conda-forge::conda-lock - conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock + micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock micromamba clean -a -y echo ">> CONDA_LOCK_START" cat environment.lock @@ -807,7 +807,7 @@ class TemplateUtilsTest extends Specification { && CONDA_OVERRIDE_CUDA="99" micromamba install -y -n base -f /scratch/conda.yml) micromamba install -y -n base conda-forge::procps-ng micromamba install -y -n base conda-forge::conda-lock - conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock + micromamba run -n base conda-lock --file /scratch/conda.yml --platform linux-64 --lockfile environment.lock micromamba clean -a -y echo ">> CONDA_LOCK_START" cat environment.lock