Ci/update refdata ga (#41)

* Adding rate matrix index (tardis-sn#2132) * adding NlteIndexHelper class * adding nlte_ionization_species to io/schemas/plasma.yml * adding nlte_excitation_species to io/schemas/plasma.yml * added nlte_ionization_species in assemble_plasma * fixed the issue with getting nlte_ionization_species from config * fixed transforming string from config to tuple for nlte ionization species * ran black * attempt of writing tests 1 * ran black * test attempt 2 * black on test_hdf_plasma * experimenting with revert * attempt 3 * reverted tardis/plasma/tests/test_complete_plasmas.py * reverted tardis/plasma/tests/test_hdf_plasma.py * adding cofig for nlte * adding fixture for tardis_cofig_verysimple_nlte * added test_plasma_nlte_section_config * ran black * fixed the issue with the test, ran it locally * ran black on necessary files * updated description in schemas * switching from nlte_ionization to be used from self * ran black * changed nlte_properties_new to nlte_solver_properties * adding nlte_rate_equation_matrix.py * reverting to previous commit * Restructuring NumbaModel (tardis-sn#2136) * Added NumbaRadial1DGeometry * Added to_numba function * Fixed incorrect naming of numba spec * Updated docstring * Updated to_numba docstring * Updated docstring * Updated numba model to contain only time explosion * updated docstring formatting error * Moved geometry to new geometry sub package * Updated all functions where numba model was used * Updated to specify units * converting time_explosion to seconds specifically * Added numba geometry fixture * Updated tests to work with numba geometry * Updated formatting * Fixed issue with geometry initialization * Fixed formatting * Add missing cell to download atom data (tardis-sn#2146) * Possible fix for prerelease workflow (tardis-sn#2127) * Possible fix for prerelease workflow * Fix double @ symbol * Changed to v2 * Pin setuptools_scm to v6 (tardis-sn#2147) * Pin setuptools_scm to v6 * Fix typo * Adding nlte_rate_equation_solver.py (tardis-sn#2140) * added nlte_rate_equation_matrix * adding the rate_equation_matrix * moved rate_matrix into a class NLTERateEquationSolver * fixed a bug in rate_matrix_index, added an example for checking if rate matrix works properly * changed the initial electron density for now * added tests, fixed a small bug * added some doctrings * fixed a typo * added some doctrings * added some doctrings part 2 * added some docstrings part 3 * removed unnecessary import * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <[email protected]> * changed how atomic number is created from rate_matrix_index * changed call of a function * got rid of unnecessary if statement in set_nlte_ion_rate * renamed last_row to charge_conservation_row * switched 0, 1 to atomic_number and ion_number to make it more readable * swtihed from rates to coefficients * changed the matrix set up to only keep necessary row for nlte_ion * ran black * fixing some doctrings * swtiched from using numbers to index names * switched the return statement to NotImplementedError * changed groupby from 0, 1 to atomic number, ion number * fixed an issue in the test * ran black Co-authored-by: Christian Vogl <[email protected]> * Set specific qgrid feedstock version (tardis-sn#2152) * Pre-release 2022.11.17 (tardis-sn#2155) Automated changes for pre-release 2022.11.17 * Post-release 2022.11.17 (tardis-sn#2156) Automated changes for post-release 2022.11.17 * Pre-release 2022.11.20 (tardis-sn#2160) Automated changes for pre-release 2022.11.20 * Fix relativistic packet initialization (tardis-sn#2159) * Fix setting of full relativity flag * Add relativistic packet source Co-authored-by: Stuart Sim <[email protected]> * Fix relativistic vpackets on inner boundary Co-authored-by: Stuart Sim <[email protected]> * Fixing typos for nlte ion (tardis-sn#2154) * fixing typos on rate_matrix * changed the np arange to use 0 instead of 0.0 * NLTE jacobian matrix (tardis-sn#2158) * added jacobian matrix and deriv block functions * added doctrings * ran black * switched from df to array * added an initial test * ran black * reorganized the tests * added doctrings * added todo comments for future work * ran black * Kilonova missing zeta (tardis-sn#2150) * solved KN ZetaData issue * KN missing Zeta fixed * mailmap changed * Pre-release 2022.12.11 (tardis-sn#2172) Automated changes for pre-release 2022.12.11 * Post-release 2022.12.12 (tardis-sn#2173) Automated changes for post-release 2022.12.12 * Add missing __init__.py files to transport and geometry subpackages (tardis-sn#2170) * Add missing __init__.py files to transport subpackage * Add missing __init__.py file to geometry subpackage * Pre-release 2022.12.25 (tardis-sn#2180) Automated changes for pre-release 2022.12.25 * Post-release 2022.12.26 (tardis-sn#2182) Automated changes for post-release 2022.12.26 * Pre-release 2023.01.08 (tardis-sn#2186) Automated changes for pre-release 2023.01.08 * Post-release 2023.01.11 (tardis-sn#2188) Automated changes for post-release 2023.01.11 * Downloading nlte_atom_data in ref data (tardis-sn#2187) adding nlte_atom_data to be downloaded * Adding nlte solver (tardis-sn#2171) * adding solver part in the calculate method * adding the objective function * added the solution vector method * final touches for the solver * tests, attempt 1 * ran black * fixed the issue with tests * ran black * added missing doctrings in the nlte_rate_equation_solver.py * added doctrings to tests * changed the test to explicitly calculate the lte solution ion number densities. * ran black * added the atom data file to download_reference_data.sh * fixed download_reference_data.sh * Revert "added the atom data file to download_reference_data.sh" This reverts commit 58ce29e. * got rid of index i, kept only shell * switched DataFrame to pandas.DataFrame in the docstrings * docstring bug fix * got rid of the deepcopy of nlte atomic data file * changed the number of shells to 5 * Update tardis/io/tests/data/tardis_configv1_nlte.yml Co-authored-by: Christian Vogl <[email protected]> * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <[email protected]> * Update tardis/io/tests/data/tardis_configv1_nlte.yml Co-authored-by: Christian Vogl <[email protected]> * Update tardis/io/tests/data/tardis_configv1_nlte.yml Co-authored-by: Christian Vogl <[email protected]> * ran black * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <[email protected]> * Update tardis/plasma/tests/test_nlte_solver.py Co-authored-by: Christian Vogl <[email protected]> * restructured a summary in a docstring for the solution_vector_block * ran black * added the test for w=0 case * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <[email protected]> * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <[email protected]> * Update tardis/plasma/tests/test_nlte_solver.py Co-authored-by: Christian Vogl <[email protected]> * fixed an issue in a docsting * fixed an issue in a docsting * removed a TODO comment Co-authored-by: Christian Vogl <[email protected]> * Rename T variables to temperature (tardis-sn#2185) * fixes tardis-sn#1600 * fixes tardis-sn#1600 * Update tardis/montecarlo/packet_source.py Co-authored-by: Atharva Arya <[email protected]> * fixes codestyle * improve codestyle * rename the function * Update packet_source.py * improve codequality * add commit * Update packet_source.py Co-authored-by: Atharva Arya <[email protected]> * Fixing test_store_runner_to_hdf (tardis-sn#2198) * checking if the object has the attribute decode * fixed another decode issue * Reading nlte_excitation_species from config (tardis-sn#2195) * implementing nlte_excitation * ran black * fixed a typo * got rid of unnecessary lines * rewrote tests * made a change on assigning the config values to plasma properties * fixed the tests * Update tardis/io/tests/test_config_reader.py Co-authored-by: Christian Vogl <[email protected]> --------- Co-authored-by: Christian Vogl <[email protected]> * Fix config reader tests (tardis-sn#2200) Fix config tests * Pre-release 2023.02.05 (tardis-sn#2205) Automated changes for pre-release 2023.02.05 * Post-release 2023.02.06 (tardis-sn#2206) Automated changes for post-release 2023.02.06 * Add version tag to simulation objects (tardis-sn#2190) * Add test for versioning info * Add version string to simulation objects * Add name to mailmap * Add another alias to mailmap * Pre-release 2023.02.12 (tardis-sn#2208) Automated changes for pre-release 2023.02.12 * Post-release 2023.02.16 (tardis-sn#2210) Automated changes for post-release 2023.02.16 * Pre-release 2023.02.19 (tardis-sn#2211) Automated changes for pre-release 2023.02.19 * Cache LFS objects in the tests workflow (tardis-sn#2194) * Cache LFS objects (actions/checkout#165) * Delete steps to see file size Delete commented step which used to download LFS objects using the bash script * Add lfs:false flag * Add my username to .mailmap * Cache hit and allow pytest to run all tests * Do git lfs checkout if the cache key is found * Post-release 2023.02.20 (tardis-sn#2213) Automated changes for post-release 2023.02.20 * Correct the description of 'no_of_packets' in Monte Carlo Configuration (tardis-sn#2214) * Correct the description of 'no_of_packets' in Monte Carlo Configuration * Added a simple description * Pre-release 2023.02.26 (tardis-sn#2222) Automated changes for pre-release 2023.02.26 * Post-release 2023.02.27 (tardis-sn#2223) Automated changes for post-release 2023.02.27 * Add docstrings to subpackages (tardis-sn#2204) * add docstring to subpackage grid * Add docstrings to subpackages * Change comments to docstrings * add docstrings to subpackages * rename gui/__init__.py * Reformat using black * add contributor infos to mailmap file * add extended summary to docstrings * Add extended summary to plasma/properties * Update tardis/io/parsers/__init__.py Co-authored-by: Sona Chitchyan <[email protected]> --------- Co-authored-by: kim <[email protected]> Co-authored-by: Sona Chitchyan <[email protected]> * Docs Fix: Download Atom Data in rpacket_tracking.ipynb (tardis-sn#2236) Download atom data from the function * Fix for automerge (tardis-sn#2242) Use gh CLI to approve pull requests; use new token * Fix for release dates (tardis-sn#2243) * MonteCarlo packet progress bar completes to 100% (tardis-sn#2237) * Refresh packet progress bar after every iteration * Udpdated .mailmap * Reformatted with black * Fix team reviewers on workflows (tardis-sn#2246) * Pre-release 2023.03.20 (tardis-sn#2247) Automated changes for pre-release 2023.03.20 * Post-release 2023.03.20 (tardis-sn#2248) Automated changes for post-release 2023.03.20 * Create new workflow * Patch for arepo tests * Restore deleted parameter * Black format; Add missing skip reason * Fix typo in comment * Add more comments * Create slash command dispatcher * Changes to dispatcher * Black format --------- Co-authored-by: Sona Chitchyan <[email protected]> Co-authored-by: Satwik Kambham <[email protected]> Co-authored-by: Andrew <[email protected]> Co-authored-by: Christian Vogl <[email protected]> Co-authored-by: tardis-bot <[email protected]> Co-authored-by: Stuart Sim <[email protected]> Co-authored-by: gleck97 <[email protected]> Co-authored-by: ABHISHEK PATIDAR <[email protected]> Co-authored-by: Atharva Arya <[email protected]> Co-authored-by: Kim <[email protected]> Co-authored-by: Abhishek Patidar <[email protected]> Co-authored-by: Le Truong <[email protected]> Co-authored-by: kim <[email protected]> Co-authored-by: Shreyas Singh <[email protected]>
epassaro · Mar 21, 2023 · 4fe9cdc · 4fe9cdc
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diff --git a/.ci-helpers/download_reference_data.sh b/.ci-helpers/download_reference_data.sh
@@ -12,10 +12,12 @@ FILES=('atom_data/kurucz_cd23_chianti_H_He.h5'
        'sdec_ref.h5'
        'unit_test_data.h5'
        'arepo_data/arepo_snapshot.hdf5'
-       'arepo_data/arepo_snapshot.json')
+       'arepo_data/arepo_snapshot.json'
+       'nlte_atom_data/TestNLTE_He_Ti.h5')
 
 mkdir -p $REF_PATH/atom_data
 mkdir -p $REF_PATH/arepo_data
+mkdir -p $REF_PATH/nlte_atom_data
 
 for FILE in "${FILES[@]}"
 do

diff --git a/.ci-helpers/get_next_version.py b/.ci-helpers/get_next_version.py
@@ -14,8 +14,11 @@
 iso_date = date(*release).isoformat()
 iso_date = iso_date.replace("-",".")
 
-version = f"{iso_date}.{str(build)}"
-version = version.rstrip(".0") if version.endswith(".0") else version
+if build > 0:
+    version = f"{iso_date}.{str(build)}"
+
+else:
+    version = iso_date
 
 print(version)
 

diff --git a/.github/workflows/dispatcher.yml b/.github/workflows/dispatcher.yml
@@ -0,0 +1,20 @@
+name: slash-command
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  dispatch:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Slash Command Dispatcher
+        uses: peter-evans/slash-command-dispatch@v3
+        with:
+          token: ${{ secrets.BOT_TOKEN }}
+          commands: |
+            update-refdata
+          repository: tardis-sn/tardis
+          issue-type: pull-request
+          permission: triage
+          allow-edits: true
+          reaction_token: ${{ secrets.BOT_TOKEN }}
diff --git a/.github/workflows/post-release.yml b/.github/workflows/post-release.yml
@@ -124,23 +124,29 @@ jobs:
             > The `post_release` workflow waits for a webhook and then updates the citation files. If the file is not modified by this pull request, please check the latest release on [Zenodo's website](https://zenodo.org/record/592480), close this pull request, and [manually run the workflow](https://docs.github.com/en/actions/managing-workflow-runs/manually-running-a-workflow).
             >
             > This pull request should be auto-merged.
-          labels: build-docs
-          reviewers: wkerzendorf, andrewfullard, epassaro
+          labels: automated, build-docs
+          team-reviewers: tardis-infrastructure
         id: create-pr
 
       - name: Wait for pull request
         run: sleep 30
 
-      - name: Approve pull request
-        uses: juliangruber/approve-pull-request-action@v1
-        with:
-          github-token: ${{ secrets.PR_APPROVAL_TOKEN }}
-          number: ${{ steps.create-pr.outputs.pull-request-number }}
+      - name: Approve pull request (I)
+        run: gh pr review ${{ steps.create-pr.outputs.pull-request-number }} --approve
+        env:
+          GITHUB_TOKEN: ${{ secrets.INFRASTRUCTURE_COORDINATOR_TOKEN }}
+        if: steps.create-pr.outputs.pull-request-operation == 'created'
+
+      - name: Approve pull request (II)
+        run: gh pr review ${{ steps.create-pr.outputs.pull-request-number }} --approve
+        env:
+          GITHUB_TOKEN: ${{ secrets.CORE_COORDINATOR_TOKEN }}
         if: steps.create-pr.outputs.pull-request-operation == 'created'
 
       - name: Enable automerge
         uses: peter-evans/enable-pull-request-automerge@v2
         with:
-          token: ${{ secrets.BOT_TOKEN }}
+          token: ${{ secrets.INFRASTRUCTURE_COORDINATOR_TOKEN }}
           pull-request-number: ${{ steps.create-pr.outputs.pull-request-number }}
           merge-method: squash
+        if: steps.create-pr.outputs.pull-request-operation == 'created'
diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml
@@ -134,23 +134,29 @@ jobs:
             > ```
             >
             > Once all the checks pass, you can safely merge this pull request manually.
-          labels: build-docs
-          reviewers: wkerzendorf, andrewfullard, epassaro
+          labels: automated, build-docs
+          team-reviewers: tardis-infrastructure
         id: create-pr
 
       - name: Wait for pull request
         run: sleep 30
 
-      - name: Approve pull request
-        uses: juliangruber/approve-pull-request-action@v1
-        with:
-          github-token: ${{ secrets.PR_APPROVAL_TOKEN }}
-          number: ${{ steps.create-pr.outputs.pull-request-number }}
+      - name: Approve pull request (I)
+        run: gh pr review ${{ steps.create-pr.outputs.pull-request-number }} --approve
+        env:
+          GITHUB_TOKEN: ${{ secrets.INFRASTRUCTURE_COORDINATOR_TOKEN }}
+        if: steps.create-pr.outputs.pull-request-operation == 'created'
+
+      - name: Approve pull request (II)
+        run: gh pr review ${{ steps.create-pr.outputs.pull-request-number }} --approve
+        env:
+          GITHUB_TOKEN: ${{ secrets.CORE_COORDINATOR_TOKEN }}
         if: steps.create-pr.outputs.pull-request-operation == 'created'
 
       - name: Enable automerge
         uses: peter-evans/enable-pull-request-automerge@v2
         with:
-          token: ${{ secrets.BOT_TOKEN }}
+          token: ${{ secrets.INFRASTRUCTURE_COORDINATOR_TOKEN }}
           pull-request-number: ${{ steps.create-pr.outputs.pull-request-number }}
           merge-method: squash
+        if: steps.create-pr.outputs.pull-request-operation == 'created'
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -28,7 +28,7 @@ jobs:
           python-version: '3.x'
 
       - name: Install setuptools_scm
-        run: pip install setuptools_scm
+        run: pip install 'setuptools_scm<7'
 
       - name: Show current version
         run: python .ci-helpers/get_current_version.py

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -47,8 +47,33 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Download reference data
-        run: bash .ci-helpers/download_reference_data.sh
+      - name: Clone tardis-sn/tardis-refdata
+        uses: actions/checkout@v2
+        with:
+          repository: tardis-sn/tardis-refdata
+          path: tardis-refdata
+          lfs: false
+
+      - name: Create LFS file list
+        run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
+        working-directory: tardis-refdata
+
+      - name: Restore LFS cache
+        uses: actions/cache@v2
+        id: lfs-cache
+        with:
+          path: tardis-refdata/.git/lfs
+          key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v1
+
+      - name: Git LFS Pull
+        run: git lfs pull
+        working-directory: tardis-refdata
+        if: steps.lfs-cache.outputs.cache-hit != 'true'
+
+      - name: Git LFS Checkout
+        run: git lfs checkout
+        working-directory: tardis-refdata
+        if: steps.lfs-cache.outputs.cache-hit == 'true'
 
       - name: Setup environment
         uses: conda-incubator/setup-miniconda@v2

diff --git a/.github/workflows/update-refdata.yml b/.github/workflows/update-refdata.yml
@@ -0,0 +1,90 @@
+#  For more information about TARDIS pipelines, please refer to:
+#
+#    https://tardis-sn.github.io/tardis/development/continuous_integration.html
+
+name: update-refdata
+
+on:
+  repository_dispatch:
+    types: [update-refdata-command]
+
+env:
+  PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata --generate-reference
+  CACHE_NUMBER: 0                       # increase to reset cache manually
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  build:
+    if: github.event_name == 'workflow_dispatch' ||
+        (github.event_name == 'pull_request' &&
+        contains(github.event.pull_request.labels.*.name, 'update-refdata'))
+
+    runs-on: ubuntu-latest
+    steps:
+
+      - uses: actions/checkout@v2
+#        if: github.event_name != 'pull_request_target'
+#
+#      - name: Checkout pull/${{ github.event.number }}
+#        uses: actions/checkout@v2
+#        with:
+#          ref: ${{ github.event.pull_request.head.sha }}
+#        if: github.event_name == 'pull_request_target'
+
+      - uses: actions/checkout@v2
+        with:
+          repository: tardis-sn/tardis-refdata
+          path: tardis-refdata
+          lfs: false
+
+      - name: Create LFS file list
+        run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
+        working-directory: tardis-refdata
+
+      - name: Restore LFS cache
+        uses: actions/cache@v2
+        id: lfs-cache
+        with:
+          path: tardis-refdata/.git/lfs
+          key: ${{ runner.os }}-lfs-${{ hashFiles('tardis-refdata/.lfs-assets-id') }}-v${{ env.CACHE_NUMBER }}
+
+      - name: Pull LFS objects
+        run: git lfs pull
+        working-directory: tardis-refdata
+        if: steps.lfs-cache.outputs.cache-hit != 'true'
+
+      - name: Checkout LFS repository
+        run: git lfs checkout
+        working-directory: tardis-refdata
+        if: steps.lfs-cache.outputs.cache-hit == 'true'
+
+      - name: Setup environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+            miniforge-variant: Mambaforge
+            miniforge-version: latest
+            activate-environment: tardis
+            use-mamba: true
+
+      - uses: actions/cache@v2
+        with:
+          path: /usr/share/miniconda3/envs/tardis
+          key: conda-linux-64-${{ hashFiles('conda-linux-64.lock') }}-v${{ env.CACHE_NUMBER }}
+        id: cache-conda
+
+      - name: Update environment
+        run: mamba update -n tardis --file conda-linux-64.lock
+        if: steps.cache-conda.outputs.cache-hit != 'true'
+
+      - name: Install package
+        run: pip install -e .
+
+      - name: Generate new reference data
+        run: pytest tardis ${{ env.PYTEST_FLAGS }}
diff --git a/.mailmap b/.mailmap
@@ -1,3 +1,4 @@
+Abhishek Patidar <[email protected]>
 Adam Suban-Loewen <[email protected]>
 
 Alexander Holas <[email protected]>
@@ -32,6 +33,7 @@ Arjun Savel <[email protected]> Arjun Savel <[email protected]
 
 Atharva Arya <[email protected]>
 Atharva Arya <[email protected]> Atharva Arya <[email protected]>
+Atharva Arya <[email protected]> atharva-2001 <[email protected]>
 Atharva Arya <[email protected]> Atharva Arya <[email protected]>
 
 Atharwa Kharkar <[email protected]>
@@ -70,6 +72,9 @@ Frederik Beaujean <[email protected]> Frederik Beaujean <[email protected]
 Gaurav Gautam <[email protected]>
 Gaurav Gautam <[email protected]> gautam1168 <[email protected]>
 
+Gerrit Leck <[email protected]>
+Gerrit Leck <[email protected]> Gerrit Leck <[email protected]>
+
 Isaac Smith <[email protected]> 
 Isaac Smith <[email protected]> Isaac Smith <[email protected]>
 Isaac Smith <[email protected]> smithis7 <[email protected]>
@@ -108,6 +113,9 @@ Kevin Cawley <[email protected]> KevinCawley <[email protected].
 
 Kevin Yap <[email protected]>
 
+Kim Lingemann <[email protected]> kimsina <[email protected]>
+Kim Lingemann <[email protected]> kim <[email protected]>
+
 Laud Bentil <[email protected]>
 Laud Bentil <[email protected]> Laud Bentil <[email protected]>
 
@@ -161,6 +169,9 @@ Sampark Sharma <[email protected]>
 Shilpi Prasad <[email protected]>
 Shilpi Prasad <[email protected]> Shilpi <[email protected]>
 
+Shreyas Singh <[email protected]>
+Shreyas Singh <[email protected]> shreyas3156 <[email protected]>
+
 Satwik Kambham <[email protected]>
 Satwik Kambham <[email protected]> code-explorer <[email protected]>
 
@@ -219,3 +230,8 @@ Youssef Eweis <[email protected]> Youssef Eweis <[email protected]
 Rohith Varma Buddaraju <[email protected]>
 Rohith Varma Buddaraju <[email protected]> rohithvarma3000 <[email protected]>
 Rohith Varma Buddaraju <[email protected]> Rohith <[email protected]>
+
+Le Truong <[email protected]>
+
+Kim Lingemann <[email protected]> kimsina <[email protected]>
+Kim Lingemann <[email protected]> kim <[email protected]>