overhaul dynamo to make it more modular

.dockerignore

@@ -0,0 +1,11 @@
+__test__
+node_modules
+.dockerignore
+.gitignore
+.github
+babel.config.js
+Dockerfile
+LICENSE
+package-lock.json
+package.json
+README.md

.github/workflows/python-docker.yml

@@ -0,0 +1,71 @@
+# This file wont do us much good in this location, make sure you change the path as directed to continue!
+
+name: Docker
+
+on:
+  push:
+    # Sequence of patterns matched against refs/tags
+    tags:
+      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+  # workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v1
+      - name: npm install and build webpack
+        run: |
+          npm install
+          npm run build
+      - uses: actions/upload-artifact@master
+        with:
+          name: webpack artifacts
+          path: public/
+  test:
+    runs-on: ubuntu-latest
+    needs: build
+    strategy:
+      matrix:
+        os: [ubuntu-lastest, windows-2016]
+        node-version: [12.x, 14.x]
+
+    steps:
+      - uses: actions/checkout@v1
+      - name: Use Node.js ${{ matrix.node-version }}
+        uses: actions/setup-node@v1
+        with:
+          node-version: ${{ matrix.node-version }}
+      - uses: actions/download-artifact@master
+        with:
+          name: webpack artifacts
+          path: public
+      - name: npm install, and test
+        run: |
+          npm install
+          npm test
+        env:
+          CI: true
+
+  Build-and-Push-Docker-Image:
+    runs-on: ubuntu-latest
+    needs: test
+    name: Docker Build, Tag, Push
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v1
+    - name: Download built artifact
+      uses: actions/download-artifact@master
+      with:
+        name: webpack artifacts
+        path: public
+    - name: Build container image
+      uses: docker/build-push-action@v1
+      with:
+        username: ${{github.actor}}
+        password: ${{secrets.GITHUB_TOKEN}}
+        registry: docker.pkg.github.com
+        repository: aristoteleo/dynamo-release
+        tag_with_sha: true

.gitignore

@@ -10,6 +10,7 @@ scripts/
 benchmarking/
 debug/
 integral_seq/
+env/
 
 dynamo.egg-info/
 dynamo_release.egg-info/
@@ -41,3 +42,8 @@ docs/source/dynamo*
 
 .coverage
 test.py
+
+# Docker related:
+node_modules/
+package-lock.json
+public/*.js

Dockerfile

@@ -0,0 +1,11 @@
+FROM python:3.6-alpine as base
+FROM base as builder
+RUN mkdir /install
+WORKDIR /install
+COPY requirements.txt /requirements.txt
+RUN pip install --install-option="--prefix=/install" -r /requirements.txt
+FROM base
+COPY --from=builder /install /usr/local
+COPY src /app
+WORKDIR /app
+CMD ["dynamo"]

docs/source/API.rst

@@ -15,6 +15,8 @@ Preprocessing (pp)
       :toctree: .
 
    pp.recipe_monocle
+   pp.cell_cycle_scores
+   pp.pca
 
 Tools (tl)
 ~~~~~~~~~~
@@ -23,100 +25,256 @@ Tools (tl)
     :maxdepth: 2
     :toctree: .
 
+   tl.neighbors
+   tl.mnn
    tl.moments
+   tl.calc_1nd_moment
+   tl.calc_2nd_moment
    tl.dynamics
 
-   tl.cell_velocities
    tl.reduceDimension
 
-   tl.gene_wise_confidence
+   tl.hdbscan
+   tl.cluster_field
+
+   tl.cell_velocities,
+   tl.confident_cell_velocities,
+
    tl.cell_wise_confidence
+   tl.gene_wise_confidence
 
+   tl.generalized_diffusion_map,
+   tl.stationary_distribution,
+   tl.diffusion,
+   tl.expected_return_time,
+
+   tl.markov_combination
+   tl.compute_markov_trans_prob
+   tl.compute_kernel_trans_prob
+   tl.compute_drift_kernel
+   tl.compute_drift_local_kernel
+   tl.compute_density_kernel
+   tl.makeTransitionMatrix
+   tl.compute_tau
+   tl.MarkovChain
+   tl.KernelMarkovChain
+   tl.DiscreteTimeMarkovChain
+   tl.ContinuousTimeMarkovChain
+
+   tl.moran_i
+   tl.find_group_markers
+   tl.two_groups_degs
+   tl.top_n_markers
+   tl.glm_degs
+
+   tl.TRNET
+   tl.trn
+   tl.sample_by_velocity
+   tl.lhsclassic
+   tl.sample
+
+   tl.converter
+
+   tl.cal_ncenter
+   tl.DDRTree
+   tl.psl
+
+Estimation (est)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Conventional scRNA-seq (csc)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: .
 
+    est.csc.sol_u
+    est.csc.sol_s
+    est.csc.sol_p
+    est.csc.fit_linreg
+    est.csc.fit_first_order_deg_lsq
+    est.csc.solve_first_order_deg
+    est.csc.fit_gamma_lsq
+    est.csc.fit_alpha_synthesis
+    est.csc.fit_alpha_degradation
+    est.csc.velocity
+    est.csc.ss_estimation
+
 Time-resolved metabolic labeling based scRNA-seq (tsc)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: .
 
+    est.tsc.kinetic_estimation,
+    est.tsc.Estimation_MomentDeg,
+    est.tsc.Estimation_MomentDegNosp,
+    est.tsc.Estimation_MomentKin,
+    est.tsc.Estimation_MomentKinNosp,
+    est.tsc.Estimation_DeterministicDeg,
+    est.tsc.Estimation_DeterministicDegNosp,
+    est.tsc.Estimation_DeterministicKinNosp,
+    est.tsc.Estimation_DeterministicKin,
+    est.tsc.GoodnessOfFit,
+
+    est.tsc.LinearODE,
+    est.tsc.Moments,
+    est.tsc.Moments_Nosplicing,
+    est.tsc.Moments_NoSwitching,
+    est.tsc.Moments_NoSwitchingNoSplicing,
+    est.tsc.Deterministic,
+    est.tsc.Deterministic_NoSplicing,
 
 Vector field (vf)
 ~~~~~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: .
 
-   vf.reconstruction
+   vf.SparseVFC
+   vf.graphize_vecfld
+   vf.vector_field_function
+   vf.VectorField
+
+   vf.FixedPoints
+   vf.VectorField2D
    vf.topography
+
+   vf.cell_accelerations
+
+   vf.speed
    vf.divergence
    vf.curl
-   vf.speed
    vf.acceleration
+   vf.curvature
    vf.torsion
    vf.Potential
 
+   vf.rank_speed_genes
+   vf.rank_divergence_genes
+   vf.rank_acceleration_genes
+   vf.rank_curvature_genes
+
+   vf.search_fixed_points
+   vf.gen_fixed_points
+   vf.gen_gradient
+   vf.IntGrad
+   vf.DiffusionMatrix
+   vf.action
+   vf.Potential
+
+   vf.path_integral
+   vf.alignment
+   vf.Wang_action
+   vf.Wang_LAP
+   vf.transition_rate
+   vf.MFPT
+   vf.Ao_pot_map
+   vf.solveQ
+
+   vf.diffusionMatrix
+
+   vf.vfGraph
+
 Prediction (pd)
 ~~~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: .
 
    pd.fate
-
    pd.fate_bias
-
+   pd.state_graph
 
 Plotting (pl)
 ~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: .
 
+   pl.basic_stats
+   pl.show_fraction
+   pl.feature_genes
+   pl.ariance_explained
+   pl.exp_by_groups
+
+   pl.cell_cycle_scores
+
    pl.scatters
    pl.phase_portraits
    pl.dynamics
-   pl.umap
+
+   pl.kinetic_curves
+   pl.kinetic_heatmap
+   pl.jacobian_kinetics
+
+   pl.pca
    pl.tsne
+   pl.umap
+   pl.trimap
+
+   pl.nneighbors
+   pl.state_graph
+
    pl.cell_wise_vectors
    pl.grid_vectors
    pl.streamline_plot
    pl.line_integral_conv
+   pl.plot_energy
+
+   pl.plot_flow_field,
+   pl.plot_fixed_points,
+   pl.plot_nullclines,
+   pl.plot_separatrix,
+   pl.plot_traj,
+   pl.topography,
+
+   pl.speed
    pl.divergence
    pl.curl
-   pl.topography
+   pl.curvature
    pl.jacobian
-   pl.nneighbors
-   pl.kinetic_curves
-   pl.kinetic_heatmap
+   pl.jacobian_heatmap
+
+   pl.show_landscape
 
+   pl.fate_bias
+
+   pl.save_fig
 
 Moive (mv)
 ~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: .
 
-   mv.fates
-
+   mv.StreamFuncAnim,
+   mv.animate_fates
 
 Simulation (sim)
 ~~~~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: .
 
+   sim.two_genes_motif
+   sim.neurogenesis
+   sim.toggle
+   sim.Ying_model
+
+   sim.Gillespie
+   sim.Simulator
+
+   sim.state_space_sampler
+   sim.evaluate
 
 External (ext)
 ~~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: .
+
     ext.ddhodge
     ext.scribe
-    ext.scifate
+    ext.mutual_inform
+    ext.scifate_glmnet