geode-gnss 1.2.48__tar.gz

geode_gnss-1.2.48/.git_archival.txt

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+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

geode_gnss-1.2.48/.gitattributes

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+.git_archival.txt  export-subst

geode_gnss-1.2.48/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug Report
+description: Create a report to help us reproduce and correct the bug
+labels: ['Bug', 'Needs Triage']
+
+body:
+- type: markdown
+  attributes:
+    value: >
+      #### Before submitting a bug, please make sure the issue hasn't been already
+      addressed by searching through [the past issues](https://github.com/demiangomez/Parallel.GAMIT/issues).
+- type: textarea
+  attributes:
+    label: Describe the bug
+    description: >
+      A clear and concise description of what the bug is.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Steps/Code to Reproduce
+    description: |
+      Please add a [minimal reproducible example](https://en.wikipedia.org/wiki/Minimal_reproducible_example) that can reproduce the error when running it. Be as succinct as possible, and include the input data that produces the bug. **Do not depend on access to postgres database**: instead you can export the input data, either as csv file using pgAdmin, or using pandas to export the relevant data. Example using pandas:
+
+      ```python
+      import psycopg2
+      import pandas as pd
+      from sqlalchemy import create_engine
+      
+      ## database credentials
+      CREDS = {
+          "host": "<HOSTNAME>",
+          "user": "<USERNAME>",
+          "port": 5432,
+          "dbname": "<DBNAME>",
+          "password": "<PASSWORD>"
+      }
+      CONNECTION_STRING = " ".join((f"{k}={v}" for k,v in CREDS.items()))
+      ENGINE = create_engine(
+          "postgresql+psycopg2://{user}:{password}@{host}:{port}/{dbname}".format(**CREDS)
+      )
+
+      # Getting data, modify this query as needed
+      query = "SELECT * FROM public.gamit where 'year'='2024' and 'doy'='044'"
+      
+      df = pd.read_sql(query, ENGINE)
+      # Modify to your output path
+      df.to_csv("/filesystem/path.csv"
+      
+      ```
+
+      Github allows you to drag the .csv file into the text box as an attachment that we can download later. If the results are short, you can also copy paste, or feel free to put it in a public gist and link it in the issue: https://gist.github.com.
+
+      In short, **we are going to run the data on just the code that is throwing the error** and we expect to get the same result as you.
+
+      We acknowledge that crafting a **minimal reproducible code example** requires some effort on your side but it really helps the maintainers quickly reproduce the problem and analyze its cause without any ambiguity. Ambiguous bug reports tend to be slower to fix because they will require more effort and back and forth discussion between the maintainers and the reporter to pin-point the precise conditions necessary to reproduce the problem.
+    placeholder: |
+      ```
+      Sample code to reproduce the problem
+      ```
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Expected Results
+    description: >
+      Please paste or describe the expected results.
+    placeholder: >
+      Example: No error is thrown.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Actual Results
+    description: |
+      Please paste or describe the results you observe instead of the expected results. If you observe an error, please paste the error message including the **full traceback** of the exception, **and the final print statement from geode**. For example:
+
+      ```python-traceback
+      ---------------------------------------------------------------------------
+      2024-10-21 09:08:16 g2global 2024 041 -> Creating network clusters
+      -- Processing type is global with 731 active stations
+      Traceback (most recent call last):
+      File "/fs/project/gomez.124/opt/conda/geode/bin/ParallelGamit.py", line 756, in
+      main()
+      File "/fs/project/gomez.124/opt/conda/geode/bin/ParallelGamit.py", line 399, in main
+      sessions = ExecuteGamit(cnn, JobServer, GamitConfig, stations, check_stations, args.ignore_missing, dates,
+      File "/fs/project/gomez.124/opt/conda/geode/bin/ParallelGamit.py", line 700, in ExecuteGamit
+      net_object = Network(cnn, archive, GamitConfig, stations, date, check_stations, ignore_missing)
+      File "/fs/project/gomez.124/opt/conda/geode/lib/python3.10/site-packages/geode/network.py", line 176, in init
+      self.sessions = self.create_gamit_sessions(cnn, archive, clusters,
+      File "/fs/project/gomez.124/opt/conda/geode/lib/python3.10/site-packages/geode/network.py", line 382, in create_gamit_sessions
+      sessions.append(GamitSession(cnn, archive, self.name, self.org,
+      File "/fs/project/gomez.124/opt/conda/geode/lib/python3.10/site-packages/geode/pyGamitSession.py", line 72, in init
+      stations_.append(stn for stn in stations if stn not in ties)
+      File "/fs/project/gomez.124/opt/conda/geode/lib/python3.10/site-packages/geode/pyStation.py", line 299, in append
+      raise pyStationException('type: ' + str(type(station)) +
+      geode.pyStation.pyStationException: type: <class 'generator'> invalid. Can only append Station objects or lists of Station objects
+      ```
+    placeholder: >
+      Please paste or specifically describe the actual output or traceback.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Versions
+    render: shell
+    description: |
+      If you built geode from the git repo, please provide the commit hash of your build; if you installed geode via pip, run the following and paste the output below.
+      ```python
+      import geode; geode.__version__
+      ```
+  validations:
+    required: true
+- type: markdown
+  attributes:
+    value: >
+      Thanks for contributing 🎉!

geode_gnss-1.2.48/.github/workflows/publish.yml

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+name: Publish
+on:
+  push:
+    tags:
+      - "1.*"
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # ← Add here (in the build job)
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+    - name: Install pypa/build
+      run: python3 -m pip install build --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    name: Publish Python 🐍 distribution 📦 to PyPI
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    
+    environment:
+      name: pypi
+      url: https://pypi.org/p/geode-gnss
+      
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: Create GitHub Release with source code
+    needs:
+      - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: gh release create '${{ github.ref_name }}' --repo '${{ github.repository }}' --notes "Release for version ${{ github.ref_name }}"

geode_gnss-1.2.48/.github/workflows/python-package-conda.yml

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+name: Python Package using Conda
+
+on:
+  push:
+    branches:
+      - 'master'
+      - 'releases/**'
+  pull_request_target:
+    types: [assigned, opened, synchronize, reopened]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update --file environment.yml --name base
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        pytest
+    - name: Coverage
+      run: |
+        conda install coverage
+        coverage run -m pytest
+        coverage report -m

geode_gnss-1.2.48/.gitignore

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+# Automated versioning files
+_version.py
+
+# JetBrains IDE files
+.idea/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+#pycharm
+.idea/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+
+# production folder in classes
+classes/production
+classes/gnss_data.cfg
+classes/error*
+.DS_Store
+
+# config files in Parallel.GAMIT folder
+parallel_gamit/gnss_data.cfg
+parallel_gamit/link_tables.sh
+
+reinstall_geode.sh
+reinstall_geode.sh

geode_gnss-1.2.48/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Gómez"
+  given-names: "Demián"
+  orcid: "https://orcid.org/0000-0002-5276-581X"
+title: "Parallel.GAMIT"
+version: 1.2.2
+date-released: 2017-12-18
+url: "https://github.com/demiangomez/Parallel.GAMIT"