From b6936ab9942f21df96c80830ab6a67d5eaec5b90 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Wed, 21 Aug 2024 13:02:41 +0200
Subject: [PATCH 01/28] Update for mamba 2.0.0rc2

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>
---
 repo2docker/buildpacks/conda/install-base-env.bash | 6 +++---
 tests/conda/py35-binder-dir/verify                 | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 4bd3add9..199d46c9 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -5,8 +5,8 @@ set -ex
 
 cd $(dirname $0)
 
-export MAMBA_VERSION=1.5.7
-export CONDA_VERSION=24.3.0
+export MAMBA_VERSION="2.0.0rc2"
+export CONDA_VERSION=24.7.1
 
 URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/${CONDA_PLATFORM}/micromamba-${MAMBA_VERSION}-0.tar.bz2"
 
@@ -36,7 +36,7 @@ update_dependencies: false
 # channel_priority: flexible
 EOT
 
-micromamba install conda=${CONDA_VERSION} mamba=${MAMBA_VERSION} -y
+micromamba install -c conda-forge/label/mamba_dev -c conda-forge conda=${CONDA_VERSION} mamba=${MAMBA_VERSION} -y
 
 echo "installing notebook env:"
 cat "${NB_ENVIRONMENT_FILE}"
diff --git a/tests/conda/py35-binder-dir/verify b/tests/conda/py35-binder-dir/verify
index 1f0ecc5f..d98403cd 100755
--- a/tests/conda/py35-binder-dir/verify
+++ b/tests/conda/py35-binder-dir/verify
@@ -21,8 +21,8 @@ assert out == "1.5.7", out
 out = sh(["mamba", "--version"])
 assert (
     out
-    == """mamba 1.5.7
-conda 24.3.0"""
+    == """mamba 2.2.0rc2
+conda 24.7.0"""
 ), out
 
 sh([kernel_python, "-c", "import numpy"])

From 39d0dd5c44573a919a755903c35ddccd480c8ba1 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Wed, 21 Aug 2024 15:00:22 +0200
Subject: [PATCH 02/28] Use conda 24.7.0

---
 repo2docker/buildpacks/conda/install-base-env.bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 199d46c9..a812571e 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -6,7 +6,7 @@ set -ex
 cd $(dirname $0)
 
 export MAMBA_VERSION="2.0.0rc2"
-export CONDA_VERSION=24.7.1
+export CONDA_VERSION=24.7.0
 
 URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/${CONDA_PLATFORM}/micromamba-${MAMBA_VERSION}-0.tar.bz2"
 

From d404831595a5b050461dafdc1e8eec2dbdde7a09 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Wed, 21 Aug 2024 15:30:27 +0200
Subject: [PATCH 03/28] Use custom build of conda-libmamba-solver

See:
https://anaconda.org/conda-canary/conda-libmamba-solver/files?channel=conda-libmamba-solver-pr-457

Co-authored-by: Hind Montassif <hind.montassif@gmail.com>

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>
---
 repo2docker/buildpacks/conda/install-base-env.bash | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index a812571e..b60e61f6 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -36,7 +36,12 @@ update_dependencies: false
 # channel_priority: flexible
 EOT
 
-micromamba install -c conda-forge/label/mamba_dev -c conda-forge conda=${CONDA_VERSION} mamba=${MAMBA_VERSION} -y
+# TODO: remove channels once 2.0.0 is used.
+micromamba install \
+    -c conda-forge/label/mamba_dev \
+    -c conda-canary/label/conda-libmamba-solver-pr-457 \
+    -c conda-forge \
+    conda=${CONDA_VERSION} mamba=${MAMBA_VERSION} -y
 
 echo "installing notebook env:"
 cat "${NB_ENVIRONMENT_FILE}"

From 6ce813d371c78f164468c1f370b634f2aff09e42 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Wed, 21 Aug 2024 15:55:55 +0200
Subject: [PATCH 04/28] Update version numbers in tests

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>
---
 tests/conda/py35-binder-dir/verify | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/conda/py35-binder-dir/verify b/tests/conda/py35-binder-dir/verify
index d98403cd..70943f91 100755
--- a/tests/conda/py35-binder-dir/verify
+++ b/tests/conda/py35-binder-dir/verify
@@ -16,12 +16,12 @@ v = out.split()[1]
 assert v[:3] == "3.5", out
 
 out = sh(["micromamba", "--version"])
-assert out == "1.5.7", out
+assert out == "2.0.0", out
 
 out = sh(["mamba", "--version"])
 assert (
     out
-    == """mamba 2.2.0rc2
+    == """mamba 2.0.0
 conda 24.7.0"""
 ), out
 

From 056740312588091b7fe353fbcfcca34b6e363619 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Wed, 21 Aug 2024 16:05:10 +0200
Subject: [PATCH 05/28] Add explicit specification for conda-libmamba-solver

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

Co-authored-by: jaimergp <jaimergp@users.noreply.github.com>
---
 repo2docker/buildpacks/conda/install-base-env.bash | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index b60e61f6..2182be77 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -36,11 +36,12 @@ update_dependencies: false
 # channel_priority: flexible
 EOT
 
-# TODO: remove channels once 2.0.0 is used.
+# TODO: remove channels and conda-libmamba-solver once 2.0.0 is used.
 micromamba install \
-    -c conda-forge/label/mamba_dev \
     -c conda-canary/label/conda-libmamba-solver-pr-457 \
+    -c conda-forge/label/mamba_dev \
     -c conda-forge \
+    "conda-libmamba-solver>=24.7.0.141" \
     conda=${CONDA_VERSION} mamba=${MAMBA_VERSION} -y
 
 echo "installing notebook env:"

From e4b24a494d183688227da715b68843bd2921da18 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Wed, 21 Aug 2024 16:20:32 +0200
Subject: [PATCH 06/28] Initialize current shell

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>
---
 repo2docker/buildpacks/conda/install-base-env.bash | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 2182be77..155dc5f1 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -23,6 +23,8 @@ chmod 0755 "$MICROMAMBA_EXE"
 
 eval "$(${MICROMAMBA_EXE} shell hook -p ${CONDA_DIR} -s posix)"
 
+eval "$(micromamba shell hook --shell )"
+
 micromamba activate
 
 export PATH="${PWD}/bin:$PATH"

From d19609bf7536dc10910a0e52c9fc255a38fa3096 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Wed, 21 Aug 2024 16:30:10 +0200
Subject: [PATCH 07/28] fixup! Initialize current shell

---
 repo2docker/buildpacks/conda/install-base-env.bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 155dc5f1..8b04552f 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -23,7 +23,7 @@ chmod 0755 "$MICROMAMBA_EXE"
 
 eval "$(${MICROMAMBA_EXE} shell hook -p ${CONDA_DIR} -s posix)"
 
-eval "$(micromamba shell hook --shell )"
+eval "$(micromamba shell hook --shell bash)"
 
 micromamba activate
 

From a947a0892d1f42cd351132bf3f7ce41b8cc994a7 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Wed, 21 Aug 2024 16:52:28 +0200
Subject: [PATCH 08/28] Adapt match specifications

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>
---
 repo2docker/buildpacks/conda/install-base-env.bash | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 8b04552f..9b494d9f 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -43,8 +43,9 @@ micromamba install \
     -c conda-canary/label/conda-libmamba-solver-pr-457 \
     -c conda-forge/label/mamba_dev \
     -c conda-forge \
-    "conda-libmamba-solver>=24.7.0.141" \
-    conda=${CONDA_VERSION} mamba=${MAMBA_VERSION} -y
+    "conda-libmamba-solver>=${CONDA_VERSION}" \
+    "conda>=${CONDA_VERSION}" \
+    mamba=${MAMBA_VERSION} -y
 
 echo "installing notebook env:"
 cat "${NB_ENVIRONMENT_FILE}"

From 6ade75f90c85b7507e19ca1b5e590487c87e86be Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Thu, 22 Aug 2024 09:18:06 +0200
Subject: [PATCH 09/28] Use `--root-prefix` flag instead of `--prefix` flag

See: https://mamba.readthedocs.io/en/latest/developer_zone/changes-2.0.html#micromamba

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

Co-authored-by: Hind Montassif <hind.montassif@gmail.com>
---
 repo2docker/buildpacks/conda/install-base-env.bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 9b494d9f..04dabf17 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -21,7 +21,7 @@ time wget -qO- ${URL} | tar -xvj bin/micromamba
 mv bin/micromamba "$MICROMAMBA_EXE"
 chmod 0755 "$MICROMAMBA_EXE"
 
-eval "$(${MICROMAMBA_EXE} shell hook -p ${CONDA_DIR} -s posix)"
+eval "$(${MICROMAMBA_EXE} shell hook --root-prefix ${CONDA_DIR} -s posix)"
 
 eval "$(micromamba shell hook --shell bash)"
 

From be0ed41510e0234f7770f8b6c3e5e75a3414c29a Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Thu, 22 Aug 2024 10:32:56 +0200
Subject: [PATCH 10/28] fixup! Use `--root-prefix` flag instead of `--prefix`
 flag

---
 repo2docker/buildpacks/conda/activate-conda.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/repo2docker/buildpacks/conda/activate-conda.sh b/repo2docker/buildpacks/conda/activate-conda.sh
index 48372318..14c46db8 100755
--- a/repo2docker/buildpacks/conda/activate-conda.sh
+++ b/repo2docker/buildpacks/conda/activate-conda.sh
@@ -1,5 +1,5 @@
 # enable conda and activate the notebook environment
-eval $(micromamba shell hook -s posix -p ${CONDA_DIR})
+eval $(micromamba shell hook -s posix -r ${CONDA_DIR})
 for name in conda mamba; do
     CONDA_PROFILE="${CONDA_DIR}/etc/profile.d/${name}.sh"
     test -f $CONDA_PROFILE && . $CONDA_PROFILE

From c19c5083d6cdfc9dc473d5ff31f6ac8ee41c9395 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Thu, 22 Aug 2024 11:22:22 +0200
Subject: [PATCH 11/28] Remove duplicated call to `micromamba shell hook`

---
 repo2docker/buildpacks/conda/install-base-env.bash | 2 --
 1 file changed, 2 deletions(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 04dabf17..178b489f 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -23,8 +23,6 @@ chmod 0755 "$MICROMAMBA_EXE"
 
 eval "$(${MICROMAMBA_EXE} shell hook --root-prefix ${CONDA_DIR} -s posix)"
 
-eval "$(micromamba shell hook --shell bash)"
-
 micromamba activate
 
 export PATH="${PWD}/bin:$PATH"

From efe36d75320d47ee371e17a7bd64183c5a47ea7c Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Thu, 22 Aug 2024 12:07:40 +0200
Subject: [PATCH 12/28] Explicitly specify the channel of the custom build of
 conda-libmamba-solver

---
 repo2docker/buildpacks/conda/install-base-env.bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 178b489f..7d55bec6 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -41,7 +41,7 @@ micromamba install \
     -c conda-canary/label/conda-libmamba-solver-pr-457 \
     -c conda-forge/label/mamba_dev \
     -c conda-forge \
-    "conda-libmamba-solver>=${CONDA_VERSION}" \
+    "conda-canary/label/conda-libmamba-solver-pr-457::conda-libmamba-solver>=${CONDA_VERSION}" \
     "conda>=${CONDA_VERSION}" \
     mamba=${MAMBA_VERSION} -y
 

From 0a14433ea8595670f7f288d07898344c656218b6 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Thu, 22 Aug 2024 17:31:03 +0200
Subject: [PATCH 13/28] Use `micromamba activate` instead of `mamba activate`

The shell macros are only defined for micromamba
but not for mamba.

This brings consistency.

But then, what was making it working before?

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

Co-authored-by: Sylvain Corlay <sylvain.corlay@gmail.com>
Co-authored-by: Hind Montassif <hind.montassif@gmail.com>
---
 repo2docker/buildpacks/conda/activate-conda.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/repo2docker/buildpacks/conda/activate-conda.sh b/repo2docker/buildpacks/conda/activate-conda.sh
index 14c46db8..15b771e7 100755
--- a/repo2docker/buildpacks/conda/activate-conda.sh
+++ b/repo2docker/buildpacks/conda/activate-conda.sh
@@ -7,8 +7,8 @@ done
 if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then
     # if the kernel is a separate env, stack them
     # so both are on PATH, notebook first
-    mamba activate ${KERNEL_PYTHON_PREFIX}
-    mamba activate --stack ${NB_PYTHON_PREFIX}
+    micromamba activate ${KERNEL_PYTHON_PREFIX}
+    micromamba activate --stack ${NB_PYTHON_PREFIX}
 
     # even though it's second on $PATH
     # make sure CONDA_DEFAULT_ENV is the *kernel* env
@@ -17,5 +17,5 @@ if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then
     # which only contains UI when the two are different
     export CONDA_DEFAULT_ENV="${KERNEL_PYTHON_PREFIX}"
 else
-    mamba activate ${NB_PYTHON_PREFIX}
+    micromamba activate ${NB_PYTHON_PREFIX}
 fi

From d520a646ffb74a509f8aa9b9047ab61a03868c30 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Thu, 22 Aug 2024 17:55:12 +0200
Subject: [PATCH 14/28] Show stdout

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>
---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d5d8dc03..50dd796d 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -91,6 +91,6 @@ jobs:
 
       - name: Run pytest
         run: |
-          pytest --verbose --color=yes --durations=10 --cov=repo2docker tests/${{ matrix.repo_type }}
+          pytest --verbose -s --color=yes --durations=10 --cov=repo2docker tests/${{ matrix.repo_type }}
 
       - uses: codecov/codecov-action@v4

From 47a1561054bc408684b7f13c81d2ac8e19b7dab4 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Thu, 22 Aug 2024 19:24:43 +0200
Subject: [PATCH 15/28] Fix version number in
 `tests/conda/py35-binder-dir/verify`

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>
---
 tests/conda/py35-binder-dir/verify | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/tests/conda/py35-binder-dir/verify b/tests/conda/py35-binder-dir/verify
index 70943f91..5fcc2860 100755
--- a/tests/conda/py35-binder-dir/verify
+++ b/tests/conda/py35-binder-dir/verify
@@ -19,10 +19,6 @@ out = sh(["micromamba", "--version"])
 assert out == "2.0.0", out
 
 out = sh(["mamba", "--version"])
-assert (
-    out
-    == """mamba 2.0.0
-conda 24.7.0"""
-), out
+assert out == "2.0.0", out
 
 sh([kernel_python, "-c", "import numpy"])

From ff16804b4b422acdbc5051b5cda51956f153c186 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Fri, 23 Aug 2024 11:51:31 +0200
Subject: [PATCH 16/28] Use micromamba instead of mamba everywhere

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

Co-authored-by: Hind Montassif <hind.montassif@gmail.com>
---
 repo2docker/buildpacks/conda/install-base-env.bash | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 7d55bec6..5023157d 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -49,7 +49,7 @@ echo "installing notebook env:"
 cat "${NB_ENVIRONMENT_FILE}"
 
 
-time ${MAMBA_EXE} create -p ${NB_PYTHON_PREFIX} --file "${NB_ENVIRONMENT_FILE}"
+time ${MICROMAMBA_EXE} create -p ${NB_PYTHON_PREFIX} --file "${NB_ENVIRONMENT_FILE}"
 
 if [[ ! -z "${NB_REQUIREMENTS_FILE:-}" ]]; then
     echo "installing pip requirements"
@@ -66,7 +66,7 @@ if [[ ! -z "${KERNEL_ENVIRONMENT_FILE:-}" ]]; then
     # install kernel env and register kernelspec
     echo "installing kernel env:"
     cat "${KERNEL_ENVIRONMENT_FILE}"
-    time ${MAMBA_EXE} create -p ${KERNEL_PYTHON_PREFIX} --file "${KERNEL_ENVIRONMENT_FILE}"
+    time ${MICROMAMBA_EXE} create -p ${KERNEL_PYTHON_PREFIX} --file "${KERNEL_ENVIRONMENT_FILE}"
 
     if [[ ! -z "${KERNEL_REQUIREMENTS_FILE:-}" ]]; then
         echo "installing pip requirements for kernel"
@@ -76,18 +76,18 @@ if [[ ! -z "${KERNEL_ENVIRONMENT_FILE:-}" ]]; then
 
     ${KERNEL_PYTHON_PREFIX}/bin/ipython kernel install --prefix "${NB_PYTHON_PREFIX}"
     echo '' > ${KERNEL_PYTHON_PREFIX}/conda-meta/history
-    ${MAMBA_EXE} list -p ${KERNEL_PYTHON_PREFIX}
+    ${MICROMAMBA_EXE} list -p ${KERNEL_PYTHON_PREFIX}
 fi
 
 # Clean things out!
-time ${MAMBA_EXE} clean --all -f -y
+time ${MICROMAMBA_EXE} clean --all -f -y
 
 # Remove the pip cache created as part of installing micromamba
 rm -rf /root/.cache
 
 chown -R $NB_USER:$NB_USER ${CONDA_DIR}
 
-${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX}
+${MICROMAMBA_EXE} list -p ${NB_PYTHON_PREFIX}
 
 # Set NPM config
 ${NB_PYTHON_PREFIX}/bin/npm config --global set prefix ${NPM_DIR}

From 19330b338ceac7a81d6649f198543854bf8e7bb5 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Mon, 26 Aug 2024 21:58:40 +0200
Subject: [PATCH 17/28] Update for rc3

---
 repo2docker/buildpacks/conda/install-base-env.bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 5023157d..7ba52431 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -5,7 +5,7 @@ set -ex
 
 cd $(dirname $0)
 
-export MAMBA_VERSION="2.0.0rc2"
+export MAMBA_VERSION="2.0.0rc3"
 export CONDA_VERSION=24.7.0
 
 URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/${CONDA_PLATFORM}/micromamba-${MAMBA_VERSION}-0.tar.bz2"

From 4a02cc38ae32b40d8b33137d0f454c952d09f78a Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Mon, 26 Aug 2024 22:11:12 +0200
Subject: [PATCH 18/28] Reuse `mamba` in the activation script

---
 repo2docker/buildpacks/conda/activate-conda.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/repo2docker/buildpacks/conda/activate-conda.sh b/repo2docker/buildpacks/conda/activate-conda.sh
index 15b771e7..14c46db8 100755
--- a/repo2docker/buildpacks/conda/activate-conda.sh
+++ b/repo2docker/buildpacks/conda/activate-conda.sh
@@ -7,8 +7,8 @@ done
 if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then
     # if the kernel is a separate env, stack them
     # so both are on PATH, notebook first
-    micromamba activate ${KERNEL_PYTHON_PREFIX}
-    micromamba activate --stack ${NB_PYTHON_PREFIX}
+    mamba activate ${KERNEL_PYTHON_PREFIX}
+    mamba activate --stack ${NB_PYTHON_PREFIX}
 
     # even though it's second on $PATH
     # make sure CONDA_DEFAULT_ENV is the *kernel* env
@@ -17,5 +17,5 @@ if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then
     # which only contains UI when the two are different
     export CONDA_DEFAULT_ENV="${KERNEL_PYTHON_PREFIX}"
 else
-    micromamba activate ${NB_PYTHON_PREFIX}
+    mamba activate ${NB_PYTHON_PREFIX}
 fi

From 14addc5a7c198a787234b55015b2b9986001a61c Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Tue, 27 Aug 2024 10:13:34 +0200
Subject: [PATCH 19/28] Revert to use MAMBA_EXE

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

Co-authored-by: Sylvain Corlay <sylvain.corlay@gmail.com>
---
 repo2docker/buildpacks/conda/install-base-env.bash | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 7ba52431..9e3b9ffa 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -49,7 +49,7 @@ echo "installing notebook env:"
 cat "${NB_ENVIRONMENT_FILE}"
 
 
-time ${MICROMAMBA_EXE} create -p ${NB_PYTHON_PREFIX} --file "${NB_ENVIRONMENT_FILE}"
+time ${MAMBA_EXE} create -p ${NB_PYTHON_PREFIX} --file "${NB_ENVIRONMENT_FILE}"
 
 if [[ ! -z "${NB_REQUIREMENTS_FILE:-}" ]]; then
     echo "installing pip requirements"
@@ -66,7 +66,7 @@ if [[ ! -z "${KERNEL_ENVIRONMENT_FILE:-}" ]]; then
     # install kernel env and register kernelspec
     echo "installing kernel env:"
     cat "${KERNEL_ENVIRONMENT_FILE}"
-    time ${MICROMAMBA_EXE} create -p ${KERNEL_PYTHON_PREFIX} --file "${KERNEL_ENVIRONMENT_FILE}"
+    time ${MAMBA_EXE} create -p ${KERNEL_PYTHON_PREFIX} --file "${KERNEL_ENVIRONMENT_FILE}"
 
     if [[ ! -z "${KERNEL_REQUIREMENTS_FILE:-}" ]]; then
         echo "installing pip requirements for kernel"
@@ -76,18 +76,18 @@ if [[ ! -z "${KERNEL_ENVIRONMENT_FILE:-}" ]]; then
 
     ${KERNEL_PYTHON_PREFIX}/bin/ipython kernel install --prefix "${NB_PYTHON_PREFIX}"
     echo '' > ${KERNEL_PYTHON_PREFIX}/conda-meta/history
-    ${MICROMAMBA_EXE} list -p ${KERNEL_PYTHON_PREFIX}
+    ${MAMBA_EXE} list -p ${KERNEL_PYTHON_PREFIX}
 fi
 
 # Clean things out!
-time ${MICROMAMBA_EXE} clean --all -f -y
+time ${MAMBA_EXE} clean --all -f -y
 
 # Remove the pip cache created as part of installing micromamba
 rm -rf /root/.cache
 
 chown -R $NB_USER:$NB_USER ${CONDA_DIR}
 
-${MICROMAMBA_EXE} list -p ${NB_PYTHON_PREFIX}
+${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX}
 
 # Set NPM config
 ${NB_PYTHON_PREFIX}/bin/npm config --global set prefix ${NPM_DIR}

From 3d7a7ccc0a4dfe4897e393c5a822a42966099a62 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Thu, 29 Aug 2024 17:37:48 +0200
Subject: [PATCH 20/28] Use 2.0.0rc4

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>
---
 repo2docker/buildpacks/conda/install-base-env.bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 9e3b9ffa..69ff4397 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -5,7 +5,7 @@ set -ex
 
 cd $(dirname $0)
 
-export MAMBA_VERSION="2.0.0rc3"
+export MAMBA_VERSION="2.0.0rc4"
 export CONDA_VERSION=24.7.0
 
 URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/${CONDA_PLATFORM}/micromamba-${MAMBA_VERSION}-0.tar.bz2"

From 0a6406cda25623f685192beeec6fccd2da9b5268 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Thu, 29 Aug 2024 18:14:31 +0200
Subject: [PATCH 21/28] Do not forward stdout

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>
---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 50dd796d..d5d8dc03 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -91,6 +91,6 @@ jobs:
 
       - name: Run pytest
         run: |
-          pytest --verbose -s --color=yes --durations=10 --cov=repo2docker tests/${{ matrix.repo_type }}
+          pytest --verbose --color=yes --durations=10 --cov=repo2docker tests/${{ matrix.repo_type }}
 
       - uses: codecov/codecov-action@v4

From 1ebc84ea04874ff98b56a1bf44cd041c0be9445d Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Fri, 30 Aug 2024 15:05:16 +0200
Subject: [PATCH 22/28] Log source of profile

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>
---
 repo2docker/buildpacks/conda/activate-conda.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/repo2docker/buildpacks/conda/activate-conda.sh b/repo2docker/buildpacks/conda/activate-conda.sh
index 14c46db8..69f3884a 100755
--- a/repo2docker/buildpacks/conda/activate-conda.sh
+++ b/repo2docker/buildpacks/conda/activate-conda.sh
@@ -2,6 +2,7 @@
 eval $(micromamba shell hook -s posix -r ${CONDA_DIR})
 for name in conda mamba; do
     CONDA_PROFILE="${CONDA_DIR}/etc/profile.d/${name}.sh"
+    echo "Activating profile: ${CONDA_PROFILE}"
     test -f $CONDA_PROFILE && . $CONDA_PROFILE
 done
 if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then

From ea839030b0594977b7ed0b92e6a01c5d903f93d2 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Fri, 30 Aug 2024 15:08:23 +0200
Subject: [PATCH 23/28] Log information of the current environment in
 py36-postBuild/postBuild

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>
---
 tests/conda/py36-postBuild/postBuild | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/conda/py36-postBuild/postBuild b/tests/conda/py36-postBuild/postBuild
index cf0db012..77983ca7 100755
--- a/tests/conda/py36-postBuild/postBuild
+++ b/tests/conda/py36-postBuild/postBuild
@@ -1,6 +1,8 @@
 #!/bin/bash
 set -ex
 
+mamba info
+
 # mamba/conda installs in kernel env
 mamba install -y make
 

From 86ff1fa27c1d6df96c2f780d7efd94a8e11df563 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Fri, 30 Aug 2024 16:06:22 +0200
Subject: [PATCH 24/28] Show all env variables

Co-authored-by: jaimergp <jaimergp@users.noreply.github.com>
---
 tests/conda/py36-postBuild/postBuild | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/conda/py36-postBuild/postBuild b/tests/conda/py36-postBuild/postBuild
index 77983ca7..d7d9bf98 100755
--- a/tests/conda/py36-postBuild/postBuild
+++ b/tests/conda/py36-postBuild/postBuild
@@ -1,6 +1,8 @@
 #!/bin/bash
 set -ex
 
+env | sort
+
 mamba info
 
 # mamba/conda installs in kernel env

From 5ce4467c4af9256e63517a1007a7c70cccc1ebb1 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Fri, 30 Aug 2024 16:15:56 +0200
Subject: [PATCH 25/28] Debug activate-conda.sh

---
 repo2docker/buildpacks/conda/activate-conda.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/repo2docker/buildpacks/conda/activate-conda.sh b/repo2docker/buildpacks/conda/activate-conda.sh
index 69f3884a..31264657 100755
--- a/repo2docker/buildpacks/conda/activate-conda.sh
+++ b/repo2docker/buildpacks/conda/activate-conda.sh
@@ -1,4 +1,5 @@
 # enable conda and activate the notebook environment
+set -ex
 eval $(micromamba shell hook -s posix -r ${CONDA_DIR})
 for name in conda mamba; do
     CONDA_PROFILE="${CONDA_DIR}/etc/profile.d/${name}.sh"

From 4a5bd4123629c777983302d6149c12eaa30d6d2b Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Fri, 13 Sep 2024 15:38:40 +0200
Subject: [PATCH 26/28] Use 2.0.0rc5

---
 repo2docker/buildpacks/conda/install-base-env.bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 69ff4397..1012743f 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -5,7 +5,7 @@ set -ex
 
 cd $(dirname $0)
 
-export MAMBA_VERSION="2.0.0rc4"
+export MAMBA_VERSION="2.0.0rc5"
 export CONDA_VERSION=24.7.0
 
 URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/${CONDA_PLATFORM}/micromamba-${MAMBA_VERSION}-0.tar.bz2"

From a41a00a92f0941a9c7cb511694b63793214ffc26 Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Fri, 13 Sep 2024 16:24:51 +0200
Subject: [PATCH 27/28] Empty commit to retrigger CI

Signed-off-by: Julien Jerphanion <git@jjerphan.xyz>

From b6a0b84360564518bd7e31b22242273afaded3ca Mon Sep 17 00:00:00 2001
From: Julien Jerphanion <git@jjerphan.xyz>
Date: Fri, 20 Sep 2024 18:53:51 +0200
Subject: [PATCH 28/28] Use 2.0.0rc6

---
 repo2docker/buildpacks/conda/install-base-env.bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash
index 1012743f..b381bbb7 100755
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@@ -5,7 +5,7 @@ set -ex
 
 cd $(dirname $0)
 
-export MAMBA_VERSION="2.0.0rc5"
+export MAMBA_VERSION="2.0.0rc6"
 export CONDA_VERSION=24.7.0
 
 URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/${CONDA_PLATFORM}/micromamba-${MAMBA_VERSION}-0.tar.bz2"