Merge pull request #9 from miguelcarcamov/development

Development

.github/workflows/build.yaml

@@ -47,17 +47,17 @@ jobs:
       run: python3 -m build
     - name: Build bdist package
       run: python3 setup.py bdist_wheel
-    - name: Install selfcalframework
+    - name: Install snow
       run: pip install dist/*.tar.gz
     - name: Upload artifacts
       uses: actions/upload-artifact@v3
       with:
-        name: selfcalframework-artifacts
+        name: snow-artifacts
         path: dist/*
     - name: Run commands to test that everything is OK
       run: |
-        pip3 freeze | grep "selfcalframework"
-        python3 -c "import selfcalframework"
+        pip3 freeze | grep "snow"
+        python3 -c "import snow"
   test:
     runs-on: ubuntu-latest
     needs: build
@@ -81,9 +81,9 @@ jobs:
     - uses: actions/download-artifact@v3
       id: download
       with:
-        name: selfcalframework-artifacts
+        name: snow-artifacts
         path: dist/
-    - name: Install selfcalframework from artifacts
+    - name: Install snow from artifacts
       run: pip3 install dist/*.tar.gz
     #- name: Test with pytest and pycov
     #  run: pytest --cov=csromer --cov-report xml:coverage.xml --cov-report term-missing tests/ -W "ignore" -v

.github/workflows/build_latest_container.yaml

@@ -51,16 +51,16 @@ jobs:
       run: python3 -m build
     - name: Build bdist package
       run: python3 setup.py bdist_wheel
-    - name: Install selfcalframework
+    - name: Install snow
       run: pip install dist/*.tar.gz
     - name: Upload artifacts
       uses: actions/upload-artifact@v3
       with:
         path: dist/*
     - name: Run commands to test that everything is finished
       run: |
-        pip3 freeze | grep "selfcalframework"
-        python3 -c "import selfcalframework"
+        pip3 freeze | grep "snow"
+        python3 -c "import snow"
   build-latest-container:
     runs-on: ubuntu-latest
     needs: build

.gitignore

@@ -128,4 +128,4 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
-!/src/selfcalframework/_version.py
+!/src/snow/_version.py

.pre-commit-config.yaml

@@ -29,5 +29,5 @@ repos:
   rev: v0.31.1
   hooks:
   - id: markdownlint-fix
-    entry: markdownlint -f '**/*.md' --disable MD013 MD036 MD046 MD033 MD041
+    entry: markdownlint -f '**/*.md' --disable MD013 MD036 MD046 MD033 MD041 MD040
         # args: [--disable MD013 MD036]

Dockerfile

@@ -38,5 +38,7 @@ RUN python3 --version
 RUN pip3 --version
 RUN python3 -m pip install --upgrade pip
 RUN python3 -m pip install mpi4py --no-cache-dir
-RUN echo "Hello from selfcalframework base image"
-LABEL org.opencontainers.image.source="https://github.com/miguelcarcamov/selfcalframework"
+RUN echo "Hello from SNOW base image"
+LABEL org.opencontainers.image.source="https://github.com/miguelcarcamov/snow"
+LABEL org.opencontainers.image.description="Container image for SNOW"
+LABEL org.opencontainers.image.licenses=GPL3

Dockerfile.prod

@@ -1,8 +1,10 @@
-FROM ghcr.io/miguelcarcamov/selfcalframework:base
+FROM ghcr.io/miguelcarcamov/snow:base
 
 RUN python3 --version
 RUN pip3 --version
-RUN echo "Installing selfcalframework"
-RUN pip3 install git+https://github.com/miguelcarcamov/selfcalframework.git
-RUN echo "Hello from selfcalframework production image"
-LABEL org.opencontainers.image.source="https://github.com/miguelcarcamov/selfcalframework"
+RUN echo "Installing snow"
+RUN pip3 install git+https://github.com/miguelcarcamov/snow.git
+RUN echo "Hello from snow production image"
+LABEL org.opencontainers.image.source="https://github.com/miguelcarcamov/snow"
+LABEL org.opencontainers.image.description="Container image for SNOW"
+LABEL org.opencontainers.image.licenses=GPL3

README.md

@@ -1,6 +1,8 @@
-# Object Oriented Framework for Self-calibration of radio-interferometric datasets
+# **SNOW**
 
-Many radioastronomers repeat the process of writing different scripts for self-calibration
+## ca**S**a pytho**N** self-calibrati**O**n frame**W**ork
+
+Many radio-astronomers repeat the process of writing different scripts for self-calibration
 depending on their datasets. This repository holds an object-oriented Framework for self-calibration
 of radio-interferometric datasets that will help radio astronomers to minimize the tedious work of
 writing self-calibration scripts once again. The idea is to call just one main Python script that
@@ -17,42 +19,41 @@ objects (phase, amplitude, amplitude-phase) having the self-calibrated dataset a
 
 ### From PYPI repository
 
-- `pip install selfcalframework`
+- `pip install snow`
 
 ### From Github
 
-- `pip install -U git+https://github.com/miguelcarcamov/selfcalframework`
+- `pip install -U git+https://github.com/miguelcarcamov/snow`
 
 ### From source
 
 ```bash
-git clone https://github.com/miguelcarcamov/selfcalframework
-cd selfcalframework
+git clone https://github.com/miguelcarcamov/snow
+cd snow
 pip install .
 ```
 
 ### From source as developer
 
 ```bash
-git clone https://github.com/miguelcarcamov/selfcalframework
-cd selfcalframework
+git clone https://github.com/miguelcarcamov/snow
+cd snow
 pip install e .
 ```
 
 ## Using docker container
 
 ```bash
-docker pull ghcr.io/miguelcarcamov/selfcalframework:latest
+docker pull ghcr.io/miguelcarcamov/snow:latest
 ```
 
-## Run selfcalframework
+## Run snow
 
-```Python
+```python
 # Import the modules that you want to use
 import sys
-import numpy as np
-from src.selfcalframework.selfcalibration import Phasecal, AmpPhasecal
-from src.selfcalframework.imaging import Tclean
+from snow.selfcalibration import Phasecal, AmpPhasecal
+from snow.imaging import Tclean
 
 if __name__ == '__main__':
  # This step is up to you, and option to capture your arguments from terminal is using sys.argv

config.py

@@ -0,0 +1,20 @@
+import time
+
+datapath = ["~/.casa/data"]
+rundata = "~/.casa/data/rsync"
+logfile = 'casalog-%s.log' % time.strftime("%Y%m%d-%H", time.localtime())
+telemetry_enabled = True
+crashreporter_enabled = True
+nologfile = False
+log2term = True
+nologger = True
+nogui = False
+colors = "LightBG"
+agg = False
+pipeline = False
+iplog = True
+user_site = False
+telemetry_log_directory = "/tmp"
+telemetry_log_limit = 20000
+telemetry_log_size_interval = 60
+telemetry_submit_interval = 604800

main_files/main_ALMA.py

@@ -1,6 +1,6 @@
 import sys
-from src.selfcalframework.imaging import Tclean
-from src.selfcalframework.selfcalibration import AmpPhasecal, Phasecal
+from snow.imaging import Tclean
+from snow.selfcalibration import AmpPhasecal, Phasecal
 
 if __name__ == '__main__':
     visfile = sys.argv[3]

main_files/main_VLA.py

@@ -1,6 +1,6 @@
 import sys
-from src.selfcalframework.imaging import Tclean
-from src.selfcalframework.selfcalibration import AmpPhasecal, Phasecal
+from snow.imaging import Tclean
+from snow.selfcalibration import AmpPhasecal, Phasecal
 
 if __name__ == '__main__':
     visfile = sys.argv[3]

main_files/main_eMERLIN.py

@@ -2,8 +2,8 @@
 import sys
 from casatasks import flagdata, mstransform, flagmanager
 
-from src.selfcalframework.imaging import Tclean
-from src.selfcalframework.selfcalibration import AmpPhasecal
+from snow.imaging import Tclean
+from snow.selfcalibration import AmpPhasecal
 
 if __name__ == '__main__':
 

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=62.6.0", "setuptools-scm", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "selfcalframework"
+name = "snow"
 authors = [
     {name = "Miguel Cárcamo", email = "[email protected]"},
 ]
@@ -25,8 +25,8 @@ Source = "https://github.com/miguelcarcamov/selfcalframework"
 
 [tool.setuptools.packages.find]
 where = ["src"]
-include = ["selfcalframework*"]
+include = ["snow*"]
 namespaces = false
 
 [tool.setuptools_scm]
-write_to = "src/selfcalframework/_version.py"
+write_to = "src/snow/_version.py"

requirements.txt

@@ -1,14 +1,14 @@
 almatasks==1.5.2
 astropy==5.1
-casadata==2022.1.17
-casampi==0.5.0
-casaplotms==1.6.2
-casaplotserver==1.2.1
-casashell==6.5.0.15
-casatasks==6.5.0.15
-casatestutils==6.5.0.15
-casatools==6.5.0.15
-casaviewer==1.5.2
+casadata==2022.9.5
+casampi==0.5.01
+casaplotms==1.8.7
+casaplotserver==1.4.6
+casashell==6.5.2.26
+casatasks==6.5.2.26
+casatestutils==6.5.2.26
+casatools==6.5.2.26
+casaviewer==1.6.6
 numpy==1.22.4
 reproject==0.9
 scipy==1.8.1

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
-name = selfcalframework
-version = attr: selfcalframework.__version__
+name = snow
+version = attr: snow.__version__
 description = A Python object oriented framework to do self-calibration
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -11,3 +11,8 @@ column_limit = 100
 dedent_closing_brackets = true
 allow_split_before_dict_value = false
 split_before_bitwise_operator = false
+
+[isort]
+multi_line_output = 3
+include_trailing_comma = true
+line_length = 100

src/selfcalframework/imaging/gpuvmem.py → src/snow/imaging/gpuvmem.py

@@ -5,34 +5,15 @@
 
 from casatasks import exportfits, fixvis, immath, importfits, tclean
 from casatools import image
+from dataclasses import dataclass, field
 
 from ..utils.image_utils import reproject
 from .imager import Imager
 
 
+@dataclass(init=False, repr=True)
 class GPUvmem(Imager):
-
-    def __init__(
-        self,
-        executable: str = "gpuvmem",
-        gpu_blocks: list = [16, 16, 256],
-        initial_values: list = [],
-        regfactors: list = [],
-        gpuids: list = [0],
-        residual_output: str = "residuals.ms",
-        model_input: str = None,
-        model_out: str = "mod_out.fits",
-        user_mask: str = None,
-        force_noise: float = None,
-        gridding_threads: int = 4,
-        positivity: bool = True,
-        ftol: float = 1e-12,
-        noise_cut: float = 10.0,
-        gridding: bool = False,
-        print_images: bool = False,
-        **kwargs
-    ):
-        """
+    """
         gpuvmem imager object
 
         Parameters
@@ -55,9 +36,54 @@ def __init__(
         noise_cut : Mask threshold based one the inverse of the primary beam
         gridding : Whether to grid visibilities or not to increase computation speed
         print_images : Whether to output the intermediate images during the optimization
-        kwargs : General imager parameters
-        """
+    """
+    executable: str = "gpuvmem"
+    gpu_blocks: list = None
+    initial_values: list = field(init=True, repr=True, default_factory=list)
+    regfactors: list = field(init=True, repr=True, default_factory=list)
+    gpuids: list = None
+    residual_output: str = "residuals.ms"
+    model_input: str = None
+    model_out: str = "mod_out.fits"
+    user_mask: str = None
+    force_noise: float = None
+    gridding_threads: int = 4
+    positivity: bool = True
+    ftol: float = 1e-12
+    noise_cut: float = 10.0
+    gridding: bool = False
+    print_images: bool = False
+
+    def __init__(
+        self,
+        executable: str = "gpuvmem",
+        gpu_blocks: list = [16, 16, 256],
+        initial_values: list = [],
+        regfactors: list = [],
+        gpuids: list = [0],
+        residual_output: str = "residuals.ms",
+        model_input: str = None,
+        model_out: str = "mod_out.fits",
+        user_mask: str = None,
+        force_noise: float = None,
+        gridding_threads: int = 4,
+        positivity: bool = True,
+        ftol: float = 1e-12,
+        noise_cut: float = 10.0,
+        gridding: bool = False,
+        print_images: bool = False,
+        **kwargs
+    ):
+
         super().__init__(**kwargs)
+        super().__post_init__()
+
+        if self.gpu_blocks is None:
+            self.gpu_blocks = [16, 16, 256]
+
+        if self.gpuids is None:
+            self.gpuids = [0]
+
         self.name = "GPUvmem"
         self.executable = executable
         self.gpu_blocks = gpu_blocks